From 583ae94b8c5870b60eb0973a29d63ae94d35f195 Mon Sep 17 00:00:00 2001 From: Mira Kuntz Date: Mon, 11 Nov 2024 10:22:13 +0100 Subject: [PATCH 1/3] reorganize subdomains for role update --- .../subdomains/africa/themes/africa.yml | 0 .../annotation/themes/annotation.yml | 10 - files/galaxy/subdomains/aqua/themes/aqua.yml | 0 .../subdomains/assembly/themes/assembly.yml | 11 - files/galaxy/subdomains/beta/themes/beta.yml | 0 .../subdomains/cancer/themes/cancer.yml | 0 .../themes/cheminformatics.yml | 0 .../subdomains/climate/themes/climate.yml | 51 -- .../subdomains/clipseq/themes/clipseq.yml | 0 .../subdomains/covid19/themes/covid19.yml | 0 .../earth-system/themes/earth-system.yml | 0 .../subdomains/ecology/themes/ecology.yml | 51 -- .../subdomains/eirene/themes/eirene.yml | 0 .../subdomains/erasmusmc/themes/erasmusmc.yml | 0 .../graphclust/themes/graphclust.yml | 0 .../hicexplorer/themes/hicexplorer.yml | 10 - .../humancellatlas/themes/humancellatlas.yml | 0 .../subdomains/imaging/themes/imaging.yml | 10 - .../galaxy/subdomains/india/themes/india.yml | 0 files/galaxy/subdomains/lite/themes/lite.yml | 0 files/galaxy/subdomains/live/themes/live.yml | 6 - .../subdomains/materials/themes/materials.yml | 0 .../metabolomics/themes/metabolomics.yml | 0 .../metagenomics/themes/metagenomics.yml | 0 .../microbiome/themes/microbiome.yml | 0 .../microgalaxy/themes/microgalaxy.yml | 0 files/galaxy/subdomains/ml/themes/ml.yml | 0 .../subdomains/nanopore/themes/nanopore.yml | 0 .../galaxy/subdomains/phage/themes/phage.yml | 0 .../subdomains/plants/themes/plants.yml | 7 - .../proteomics/themes/proteomics.yml | 0 files/galaxy/subdomains/rna/themes/rna.yml | 0 .../singlecell/themes/singlecell.yml | 3 - .../spatialomics/themes/spatialomics.yml | 0 .../streetscience/themes/streetscience.yml | 0 files/galaxy/subdomains/test/themes/test.yml | 0 .../subdomains/virology/themes/virology.yml | 12 - group_vars/sn06.yml | 39 -- group_vars/sn06/sn06.yml | 435 ++++++++++++++++++ group_vars/sn06/subdomains.yml | 222 +++++++++ requirements.yaml | 2 +- sn06.yml | 3 - 42 files changed, 658 insertions(+), 214 deletions(-) delete mode 100644 files/galaxy/subdomains/africa/themes/africa.yml delete mode 100644 files/galaxy/subdomains/annotation/themes/annotation.yml delete mode 100644 files/galaxy/subdomains/aqua/themes/aqua.yml delete mode 100644 files/galaxy/subdomains/assembly/themes/assembly.yml delete mode 100644 files/galaxy/subdomains/beta/themes/beta.yml delete mode 100644 files/galaxy/subdomains/cancer/themes/cancer.yml delete mode 100644 files/galaxy/subdomains/cheminformatics/themes/cheminformatics.yml delete mode 100644 files/galaxy/subdomains/climate/themes/climate.yml delete mode 100644 files/galaxy/subdomains/clipseq/themes/clipseq.yml delete mode 100644 files/galaxy/subdomains/covid19/themes/covid19.yml delete mode 100644 files/galaxy/subdomains/earth-system/themes/earth-system.yml delete mode 100644 files/galaxy/subdomains/ecology/themes/ecology.yml delete mode 100644 files/galaxy/subdomains/eirene/themes/eirene.yml delete mode 100644 files/galaxy/subdomains/erasmusmc/themes/erasmusmc.yml delete mode 100644 files/galaxy/subdomains/graphclust/themes/graphclust.yml delete mode 100644 files/galaxy/subdomains/hicexplorer/themes/hicexplorer.yml delete mode 100644 files/galaxy/subdomains/humancellatlas/themes/humancellatlas.yml delete mode 100644 files/galaxy/subdomains/imaging/themes/imaging.yml delete mode 100644 files/galaxy/subdomains/india/themes/india.yml delete mode 100644 files/galaxy/subdomains/lite/themes/lite.yml delete mode 100644 files/galaxy/subdomains/live/themes/live.yml delete mode 100644 files/galaxy/subdomains/materials/themes/materials.yml delete mode 100644 files/galaxy/subdomains/metabolomics/themes/metabolomics.yml delete mode 100644 files/galaxy/subdomains/metagenomics/themes/metagenomics.yml delete mode 100644 files/galaxy/subdomains/microbiome/themes/microbiome.yml delete mode 100644 files/galaxy/subdomains/microgalaxy/themes/microgalaxy.yml delete mode 100644 files/galaxy/subdomains/ml/themes/ml.yml delete mode 100644 files/galaxy/subdomains/nanopore/themes/nanopore.yml delete mode 100644 files/galaxy/subdomains/phage/themes/phage.yml delete mode 100644 files/galaxy/subdomains/plants/themes/plants.yml delete mode 100644 files/galaxy/subdomains/proteomics/themes/proteomics.yml delete mode 100644 files/galaxy/subdomains/rna/themes/rna.yml delete mode 100644 files/galaxy/subdomains/singlecell/themes/singlecell.yml delete mode 100644 files/galaxy/subdomains/spatialomics/themes/spatialomics.yml delete mode 100644 files/galaxy/subdomains/streetscience/themes/streetscience.yml delete mode 100644 files/galaxy/subdomains/test/themes/test.yml delete mode 100644 files/galaxy/subdomains/virology/themes/virology.yml create mode 100644 group_vars/sn06/sn06.yml create mode 100644 group_vars/sn06/subdomains.yml diff --git a/files/galaxy/subdomains/africa/themes/africa.yml b/files/galaxy/subdomains/africa/themes/africa.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/annotation/themes/annotation.yml b/files/galaxy/subdomains/annotation/themes/annotation.yml deleted file mode 100644 index 5b4c5abc2..000000000 --- a/files/galaxy/subdomains/annotation/themes/annotation.yml +++ /dev/null @@ -1,10 +0,0 @@ -annotation: - masthead: - color: > - linear-gradient(to right, #3337 0, #3337 365px, transparent 365px), - linear-gradient(to left, #3337 0, #3337 120px, transparent 120px), - left / 23% url("/static/dist/annotation.png") - link: - color: "#3337" - hover: "#3339" - active: "#333e" diff --git a/files/galaxy/subdomains/aqua/themes/aqua.yml b/files/galaxy/subdomains/aqua/themes/aqua.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/assembly/themes/assembly.yml b/files/galaxy/subdomains/assembly/themes/assembly.yml deleted file mode 100644 index d175f6abb..000000000 --- a/files/galaxy/subdomains/assembly/themes/assembly.yml +++ /dev/null @@ -1,11 +0,0 @@ -assembly: - masthead: - color: > - bottom -90px left / 1000px no-repeat url("/static/dist/flying-bird-1.svg"), - bottom -90px left / 1000px no-repeat url("/static/dist/flying-bird-2.svg"), - linear-gradient( 20deg, - rgb(7, 40, 98) 0%, - rgb(69, 122, 184) 48%, - rgba(165, 204, 210, 0.9676562309265136) 74%, - rgb(228, 195, 131) 92%, - rgb(203, 119, 79) 100%) diff --git a/files/galaxy/subdomains/beta/themes/beta.yml b/files/galaxy/subdomains/beta/themes/beta.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/cancer/themes/cancer.yml b/files/galaxy/subdomains/cancer/themes/cancer.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/cheminformatics/themes/cheminformatics.yml b/files/galaxy/subdomains/cheminformatics/themes/cheminformatics.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/climate/themes/climate.yml b/files/galaxy/subdomains/climate/themes/climate.yml deleted file mode 100644 index b54b380e8..000000000 --- a/files/galaxy/subdomains/climate/themes/climate.yml +++ /dev/null @@ -1,51 +0,0 @@ -climate: - masthead: - color: > - linear-gradient(to right, #3337 0, #3337 340px, transparent 340px), - linear-gradient(to left, #3337 0, #3337 120px, transparent 120px), - linear-gradient(to right, #2171b5 0.00%, - #2171b5 0.83%, #c6dbef 0.83%, #c6dbef 1.65%, #9ecae1 1.65%, #9ecae1 2.48%, #fee0d2 2.48%, - #fee0d2 3.31%, #6baed6 3.31%, #6baed6 4.13%, #9ecae1 4.13%, #9ecae1 4.96%, #08519c 4.96%, - #08519c 5.79%, #08306b 5.79%, #08306b 6.61%, #2171b5 6.61%, #2171b5 7.44%, #4292c6 7.44%, - #4292c6 8.26%, #9ecae1 8.26%, #9ecae1 9.09%, #2171b5 9.09%, #2171b5 9.92%, #4292c6 9.92%, - #4292c6 10.74%, #9ecae1 10.74%, #9ecae1 11.57%, #deebf7 11.57%, #deebf7 12.40%, #9ecae1 12.40%, - #9ecae1 13.22%, #deebf7 13.22%, #deebf7 14.05%, #4292c6 14.05%, #4292c6 14.88%, #08519c 14.88%, - #08519c 15.70%, #deebf7 15.70%, #deebf7 16.53%, #9ecae1 16.53%, #9ecae1 17.36%, #c6dbef 17.36%, - #c6dbef 18.18%, #6baed6 18.18%, #6baed6 19.01%, #4292c6 19.01%, #4292c6 19.83%, #2171b5 19.83%, - #2171b5 20.66%, #deebf7 20.66%, #deebf7 21.49%, #fcbba1 21.49%, #fcbba1 22.31%, #9ecae1 22.31%, - #9ecae1 23.14%, #deebf7 23.14%, #deebf7 23.97%, #9ecae1 23.97%, #9ecae1 24.79%, #deebf7 24.79%, - #deebf7 25.62%, #4292c6 25.62%, #4292c6 26.45%, #deebf7 26.45%, #deebf7 27.27%, #2171b5 27.27%, - #2171b5 28.10%, #fee0d2 28.10%, #fee0d2 28.93%, #fcbba1 28.93%, #fcbba1 29.75%, #08519c 29.75%, - #08519c 30.58%, #9ecae1 30.58%, #9ecae1 31.40%, #4292c6 31.40%, #4292c6 32.23%, #c6dbef 32.23%, - #c6dbef 33.06%, #fee0d2 33.06%, #fee0d2 33.88%, #9ecae1 33.88%, #9ecae1 34.71%, #c6dbef 34.71%, - #c6dbef 35.54%, #2171b5 35.54%, #2171b5 36.36%, #fcbba1 36.36%, #fcbba1 37.19%, #4292c6 37.19%, - #4292c6 38.02%, #c6dbef 38.02%, #c6dbef 38.84%, #4292c6 38.84%, #4292c6 39.67%, #ef3b2c 39.67%, - #ef3b2c 40.50%, #deebf7 40.50%, #deebf7 41.32%, #fee0d2 41.32%, #fee0d2 42.15%, #c6dbef 42.15%, - #c6dbef 42.98%, #08306b 42.98%, #08306b 43.80%, #08519c 43.80%, #08519c 44.63%, #2171b5 44.63%, - #2171b5 45.45%, #fcbba1 45.45%, #fcbba1 46.28%, #c6dbef 46.28%, #c6dbef 47.11%, #fcbba1 47.11%, - #fcbba1 47.93%, #deebf7 47.93%, #deebf7 48.76%, #fcbba1 48.76%, #fcbba1 49.59%, #fc9272 49.59%, - #fc9272 50.41%, #fee0d2 50.41%, #fee0d2 51.24%, #9ecae1 51.24%, #9ecae1 52.07%, #fcbba1 52.07%, - #fcbba1 52.89%, #6baed6 52.89%, #6baed6 53.72%, #4292c6 53.72%, #4292c6 54.55%, #08306b 54.55%, - #08306b 55.37%, #fee0d2 55.37%, #fee0d2 56.20%, #c6dbef 56.20%, #c6dbef 57.02%, #fcbba1 57.02%, - #fcbba1 57.85%, #deebf7 57.85%, #deebf7 58.68%, #fcbba1 58.68%, #fcbba1 59.50%, #08519c 59.50%, - #08519c 60.33%, #9ecae1 60.33%, #9ecae1 61.16%, #4292c6 61.16%, #4292c6 61.98%, #deebf7 61.98%, - #deebf7 62.81%, #fcbba1 62.81%, #fcbba1 63.64%, #9ecae1 63.64%, #9ecae1 64.46%, #6baed6 64.46%, - #6baed6 65.29%, #deebf7 65.29%, #deebf7 66.12%, #6baed6 66.12%, #6baed6 66.94%, #c6dbef 66.94%, - #c6dbef 67.77%, #fcbba1 67.77%, #fcbba1 68.60%, #deebf7 68.60%, #deebf7 69.42%, #fee0d2 69.42%, - #fee0d2 70.25%, #6baed6 70.25%, #6baed6 71.07%, #4292c6 71.07%, #4292c6 71.90%, #c6dbef 71.90%, - #c6dbef 72.73%, #fcbba1 72.73%, #fcbba1 73.55%, #9ecae1 73.55%, #9ecae1 74.38%, #2171b5 74.38%, - #2171b5 75.21%, #9ecae1 75.21%, #9ecae1 76.03%, #2171b5 76.03%, #2171b5 76.86%, #fc9272 76.86%, - #fc9272 77.69%, #ef3b2c 77.69%, #ef3b2c 78.51%, #c6dbef 78.51%, #c6dbef 79.34%, #fb6a4a 79.34%, - #fb6a4a 80.17%, #deebf7 80.17%, #deebf7 80.99%, #cb181d 80.99%, #cb181d 81.82%, #fcbba1 81.82%, - #fcbba1 82.64%, #08519c 82.64%, #08519c 83.47%, #fcbba1 83.47%, #fcbba1 84.30%, #fc9272 84.30%, - #fc9272 85.12%, #ef3b2c 85.12%, #ef3b2c 85.95%, #cb181d 85.95%, #cb181d 86.78%, #fcbba1 86.78%, - #fcbba1 87.60%, #ef3b2c 87.60%, #ef3b2c 88.43%, #fb6a4a 88.43%, #fb6a4a 89.26%, #fcbba1 89.26%, - #fcbba1 90.08%, #ef3b2c 90.08%, #ef3b2c 90.91%, #cb181d 90.91%, #cb181d 91.74%, #ef3b2c 91.74%, - #ef3b2c 92.56%, #fc9272 92.56%, #fc9272 93.39%, #6baed6 93.39%, #6baed6 94.21%, #ef3b2c 94.21%, - #ef3b2c 95.04%, #fc9272 95.04%, #fc9272 95.87%, #fee0d2 95.87%, #fee0d2 96.69%, #67000d 96.69%, - #67000d 97.52%, #cb181d 97.52%, #cb181d 98.35%, #ef3b2c 98.35%, #ef3b2c 99.17%, #67000d 99.17%, - #67000d 100.00%) - link: - color: "#3337" - hover: "#3339" - active: "#333e" diff --git a/files/galaxy/subdomains/clipseq/themes/clipseq.yml b/files/galaxy/subdomains/clipseq/themes/clipseq.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/covid19/themes/covid19.yml b/files/galaxy/subdomains/covid19/themes/covid19.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/earth-system/themes/earth-system.yml b/files/galaxy/subdomains/earth-system/themes/earth-system.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/ecology/themes/ecology.yml b/files/galaxy/subdomains/ecology/themes/ecology.yml deleted file mode 100644 index c58001d9b..000000000 --- a/files/galaxy/subdomains/ecology/themes/ecology.yml +++ /dev/null @@ -1,51 +0,0 @@ -ecology: - masthead: - color: > - linear-gradient(to right, #3337 0, #3337 340px, transparent 340px), - linear-gradient(to left, #3337 0, #3337 120px, transparent 120px), - linear-gradient(to right, #2171b5 0.00%, - #2171b5 0.83%, #c6dbef 0.83%, #c6dbef 1.65%, #9ecae1 1.65%, #9ecae1 2.48%, #fee0d2 2.48%, - #fee0d2 3.31%, #6baed6 3.31%, #6baed6 4.13%, #9ecae1 4.13%, #9ecae1 4.96%, #08519c 4.96%, - #08519c 5.79%, #08306b 5.79%, #08306b 6.61%, #2171b5 6.61%, #2171b5 7.44%, #4292c6 7.44%, - #4292c6 8.26%, #9ecae1 8.26%, #9ecae1 9.09%, #2171b5 9.09%, #2171b5 9.92%, #4292c6 9.92%, - #4292c6 10.74%, #9ecae1 10.74%, #9ecae1 11.57%, #deebf7 11.57%, #deebf7 12.40%, #9ecae1 12.40%, - #9ecae1 13.22%, #deebf7 13.22%, #deebf7 14.05%, #4292c6 14.05%, #4292c6 14.88%, #08519c 14.88%, - #08519c 15.70%, #deebf7 15.70%, #deebf7 16.53%, #9ecae1 16.53%, #9ecae1 17.36%, #c6dbef 17.36%, - #c6dbef 18.18%, #6baed6 18.18%, #6baed6 19.01%, #4292c6 19.01%, #4292c6 19.83%, #2171b5 19.83%, - #2171b5 20.66%, #deebf7 20.66%, #deebf7 21.49%, #fcbba1 21.49%, #fcbba1 22.31%, #9ecae1 22.31%, - 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#fc9272 50.41%, #fee0d2 50.41%, #fee0d2 51.24%, #9ecae1 51.24%, #9ecae1 52.07%, #fcbba1 52.07%, - #fcbba1 52.89%, #6baed6 52.89%, #6baed6 53.72%, #4292c6 53.72%, #4292c6 54.55%, #08306b 54.55%, - #08306b 55.37%, #fee0d2 55.37%, #fee0d2 56.20%, #c6dbef 56.20%, #c6dbef 57.02%, #fcbba1 57.02%, - #fcbba1 57.85%, #deebf7 57.85%, #deebf7 58.68%, #fcbba1 58.68%, #fcbba1 59.50%, #08519c 59.50%, - #08519c 60.33%, #9ecae1 60.33%, #9ecae1 61.16%, #4292c6 61.16%, #4292c6 61.98%, #deebf7 61.98%, - #deebf7 62.81%, #fcbba1 62.81%, #fcbba1 63.64%, #9ecae1 63.64%, #9ecae1 64.46%, #6baed6 64.46%, - #6baed6 65.29%, #deebf7 65.29%, #deebf7 66.12%, #6baed6 66.12%, #6baed6 66.94%, #c6dbef 66.94%, - #c6dbef 67.77%, #fcbba1 67.77%, #fcbba1 68.60%, #deebf7 68.60%, #deebf7 69.42%, #fee0d2 69.42%, - #fee0d2 70.25%, #6baed6 70.25%, #6baed6 71.07%, #4292c6 71.07%, #4292c6 71.90%, #c6dbef 71.90%, - #c6dbef 72.73%, #fcbba1 72.73%, #fcbba1 73.55%, #9ecae1 73.55%, #9ecae1 74.38%, #2171b5 74.38%, - #2171b5 75.21%, #9ecae1 75.21%, #9ecae1 76.03%, #2171b5 76.03%, #2171b5 76.86%, #fc9272 76.86%, - #fc9272 77.69%, #ef3b2c 77.69%, #ef3b2c 78.51%, #c6dbef 78.51%, #c6dbef 79.34%, #fb6a4a 79.34%, - #fb6a4a 80.17%, #deebf7 80.17%, #deebf7 80.99%, #cb181d 80.99%, #cb181d 81.82%, #fcbba1 81.82%, - #fcbba1 82.64%, #08519c 82.64%, #08519c 83.47%, #fcbba1 83.47%, #fcbba1 84.30%, #fc9272 84.30%, - #fc9272 85.12%, #ef3b2c 85.12%, #ef3b2c 85.95%, #cb181d 85.95%, #cb181d 86.78%, #fcbba1 86.78%, - #fcbba1 87.60%, #ef3b2c 87.60%, #ef3b2c 88.43%, #fb6a4a 88.43%, #fb6a4a 89.26%, #fcbba1 89.26%, - #fcbba1 90.08%, #ef3b2c 90.08%, #ef3b2c 90.91%, #cb181d 90.91%, #cb181d 91.74%, #ef3b2c 91.74%, - #ef3b2c 92.56%, #fc9272 92.56%, #fc9272 93.39%, #6baed6 93.39%, #6baed6 94.21%, #ef3b2c 94.21%, - #ef3b2c 95.04%, #fc9272 95.04%, #fc9272 95.87%, #fee0d2 95.87%, #fee0d2 96.69%, #67000d 96.69%, - #67000d 97.52%, #cb181d 97.52%, #cb181d 98.35%, #ef3b2c 98.35%, #ef3b2c 99.17%, #67000d 99.17%, - #67000d 100.00%) - link: - color: "#3337" - hover: "#3339" - active: "#333e" diff --git a/files/galaxy/subdomains/eirene/themes/eirene.yml b/files/galaxy/subdomains/eirene/themes/eirene.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/erasmusmc/themes/erasmusmc.yml b/files/galaxy/subdomains/erasmusmc/themes/erasmusmc.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/graphclust/themes/graphclust.yml b/files/galaxy/subdomains/graphclust/themes/graphclust.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/hicexplorer/themes/hicexplorer.yml b/files/galaxy/subdomains/hicexplorer/themes/hicexplorer.yml deleted file mode 100644 index b44473bbd..000000000 --- a/files/galaxy/subdomains/hicexplorer/themes/hicexplorer.yml +++ /dev/null @@ -1,10 +0,0 @@ -hicexplorer: - masthead: - color: > - linear-gradient(to right, #3337 0, #3337 285px, transparent 285px), - linear-gradient(to left, #3337 0, #3337 120px, transparent 120px), - left / 340px url("/static/dist/hicexplorer.png") - link: - color: "#3337" - hover: "#3339" - active: "#333e" diff --git a/files/galaxy/subdomains/humancellatlas/themes/humancellatlas.yml b/files/galaxy/subdomains/humancellatlas/themes/humancellatlas.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/imaging/themes/imaging.yml b/files/galaxy/subdomains/imaging/themes/imaging.yml deleted file mode 100644 index 189864c10..000000000 --- a/files/galaxy/subdomains/imaging/themes/imaging.yml +++ /dev/null @@ -1,10 +0,0 @@ -imaging: - masthead: - color: > - linear-gradient(90deg, - rgb(0, 0, 0) 0%, - rgb(0, 69, 227) 17%, - rgb(9, 121, 33) 30%, - rgb(180, 170, 15) 70%, - rgb(193, 35, 0) 79%, - rgb(0, 0, 0) 100%) diff --git a/files/galaxy/subdomains/india/themes/india.yml b/files/galaxy/subdomains/india/themes/india.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/lite/themes/lite.yml b/files/galaxy/subdomains/lite/themes/lite.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/live/themes/live.yml b/files/galaxy/subdomains/live/themes/live.yml deleted file mode 100644 index 06ba27f1b..000000000 --- a/files/galaxy/subdomains/live/themes/live.yml +++ /dev/null @@ -1,6 +0,0 @@ -live: - masthead: - color: > - linear-gradient(33deg, rgba(131,58,180,1) 0%, - rgba(253,29,29,1) 25%, rgba(252,176,69,1) 50%, - rgba(253,29,29,1) 75%, rgba(131,58,180,1) 100%) diff --git a/files/galaxy/subdomains/materials/themes/materials.yml b/files/galaxy/subdomains/materials/themes/materials.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/metabolomics/themes/metabolomics.yml b/files/galaxy/subdomains/metabolomics/themes/metabolomics.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/metagenomics/themes/metagenomics.yml b/files/galaxy/subdomains/metagenomics/themes/metagenomics.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/microbiome/themes/microbiome.yml b/files/galaxy/subdomains/microbiome/themes/microbiome.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/microgalaxy/themes/microgalaxy.yml b/files/galaxy/subdomains/microgalaxy/themes/microgalaxy.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/ml/themes/ml.yml b/files/galaxy/subdomains/ml/themes/ml.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/nanopore/themes/nanopore.yml b/files/galaxy/subdomains/nanopore/themes/nanopore.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/phage/themes/phage.yml b/files/galaxy/subdomains/phage/themes/phage.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/plants/themes/plants.yml b/files/galaxy/subdomains/plants/themes/plants.yml deleted file mode 100644 index f8098bc3e..000000000 --- a/files/galaxy/subdomains/plants/themes/plants.yml +++ /dev/null @@ -1,7 +0,0 @@ -plants: - masthead: - color: > - linear-gradient(90deg, - #1a5d1a 0%, - #369c36 50%, - rgb(29 95 28) 100%) diff --git a/files/galaxy/subdomains/proteomics/themes/proteomics.yml b/files/galaxy/subdomains/proteomics/themes/proteomics.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/rna/themes/rna.yml b/files/galaxy/subdomains/rna/themes/rna.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/singlecell/themes/singlecell.yml b/files/galaxy/subdomains/singlecell/themes/singlecell.yml deleted file mode 100644 index ed5306787..000000000 --- a/files/galaxy/subdomains/singlecell/themes/singlecell.yml +++ /dev/null @@ -1,3 +0,0 @@ -singlecell: - masthead: - color: "#530080" diff --git a/files/galaxy/subdomains/spatialomics/themes/spatialomics.yml b/files/galaxy/subdomains/spatialomics/themes/spatialomics.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/streetscience/themes/streetscience.yml b/files/galaxy/subdomains/streetscience/themes/streetscience.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/test/themes/test.yml b/files/galaxy/subdomains/test/themes/test.yml deleted file mode 100644 index e69de29bb..000000000 diff --git a/files/galaxy/subdomains/virology/themes/virology.yml b/files/galaxy/subdomains/virology/themes/virology.yml deleted file mode 100644 index d355ecabe..000000000 --- a/files/galaxy/subdomains/virology/themes/virology.yml +++ /dev/null @@ -1,12 +0,0 @@ -virology: - masthead: - color: > - linear-gradient(50deg, - hsl(240deg 100% 20%) 0%, - hsl(234deg 95% 23%) 13%, - hsl(227deg 90% 26%) 26%, - hsl(220deg 85% 29%) 38%, - hsl(213deg 79% 32%) 52%, - hsl(207deg 74% 35%) 66%, - hsl(200deg 69% 38%) 82%, - hsl(194deg 64% 42%) 100%) diff --git a/group_vars/sn06.yml b/group_vars/sn06.yml index b31b8476b..226bda691 100644 --- a/group_vars/sn06.yml +++ b/group_vars/sn06.yml @@ -336,45 +336,6 @@ galaxy_themes_ansible_file_path: /scratch/workspace/usegalaxy-eu/playbooks/sn06/ galaxy_themes_conf_path: files/galaxy/config/themes_conf.yml galaxy_themes_default_welcome: https://galaxyproject.org/bare/eu/usegalaxy/main/ galaxy_themes_welcome_url_prefix: https://usegalaxy-eu.github.io/index- -galaxy_themes_subdomains: - - name: assembly - - name: nanopore - - name: erasmusmc - - name: climate - - name: hicexplorer - - name: annotation - - name: metabolomics - - name: metagenomics - - name: microbiome - - name: microgalaxy - - name: rna - - name: graphclust - - name: ecology - - name: proteomics - - name: clipseq - - name: cheminformatics - - name: imaging - - name: test - - name: beta - - name: streetscience - - name: singlecell - - name: humancellatlas - - name: ml - - name: live - - name: plants - - name: virology - - name: lite - - name: covid19 - - name: africa - - name: india - - name: spatialomics - - name: materials - - name: phage - - name: earth-system - - name: cancer - - name: aqua - - name: eirene - galaxy_config_file_src_dir: files/galaxy galaxy_config_files: diff --git a/group_vars/sn06/sn06.yml b/group_vars/sn06/sn06.yml new file mode 100644 index 000000000..226bda691 --- /dev/null +++ b/group_vars/sn06/sn06.yml @@ -0,0 +1,435 @@ +--- +# packages +software_groups_to_install: + - admin + - debug + - editors + - pdf_export_deps + - services + - terminals + - utils + +# Docker +docker_users: + - galaxy + +# Autofs +autofs_service.install: true +autofs_service.enable: true +nfs_kernel_tuning: true + +autofs_mount_points: + - data + - gxtest + - gxkey + - jwd + - usrlocal + +# Miniconda role variables (galaxyproject.miniconda) +conda_prefix: /opt/miniconda + +# fs-maintenance +fsm_maintenance_dir: "/data/dnb01/maintenance" +fsm_cron_tasks: + docker: + enable: true + name: "Docker clean up" + minute: 30 + hour: 2 + dom: "*" + month: "*" + dow: "*" + job: ". {{ galaxy_root }}/.bashrc && docker system prune -f > /dev/null" + user: "{{ fsm_galaxy_user.username }}" + gxadmin: + enable: true + name: "Gxadmin Galaxy clean up" + minute: 0 + hour: 0 + dom: "*/2" + month: "*" + dow: "*" + job: "{{ custom_telegraf_env }} /usr/bin/gxadmin galaxy cleanup 60" + user: "{{ fsm_galaxy_user.username }}" + +# TIaaS +tiaas_virtualenv_python: "python3.8" + +# Telegraf +telegraf_agent_hostname: "{{ hostname }}" +telegraf_agent_version: 1.17.2 +custom_telegraf_env: "/usr/bin/env GDPR_MODE=1 PGUSER={{ galaxy_user.name }} PGHOST={{ postgres_host }} GALAXY_ROOT={{ galaxy_server_dir }} GALAXY_CONFIG_FILE={{ galaxy_config_file }} GALAXY_LOG_DIR={{ galaxy_log_dir }} GXADMIN_PYTHON={{ galaxy_venv_dir }}/bin/python" +telegraf_plugins_extra: + listen_galaxy_routes: + plugin: "statsd" + config: + - service_address = ":8125" + - percentiles = [90] + - metric_separator = "." + - allowed_pending_messages = 10000 + - percentile_limit = 100 + + # Some custom galaxy monitoring stuff that can only run on the Galaxy server + galaxy_lastlog: + plugin: "exec" + config: + - commands = ["{{ custom_telegraf_env }} /usr/bin/gxadmin gunicorn lastlog"] + - timeout = "15s" + - data_format = "influx" + - interval = "15s" + galaxy_active_users: + plugin: "exec" + config: + - commands = ["/usr/bin/gxadmin gunicorn active-users"] + - timeout = "90s" + - data_format = "influx" + - interval = "5m" + +# Custom pip installer +pip_venv_path: "{{ galaxy_venv_dir }}" +pip_install_dependencies: + # celery and flower + - redis + - flower + # phdcomics + - beautifulsoup4 + # Used by code_files for apollo + - biopython + - bcbio-gff + # Needed for tool watching + - watchdog + # Needed gxadmin graphs + - data_hacks + # used by reports + - WeasyPrint + - nbconvert + - gitlab-arc-fs + # Needed for usegalaxy-eu.vgcn-monitoring Telegraf role + - pyyaml + - GitPython + - python-openstackclient + # WallE + - tqdm # progress bar, has no dependencies + +yum_exclude_repos: + - condor* + - npm* + +all_yum_repositories: + - name: galaxy_gpel + description: Galaxy Packages for Enterprise Linux $releasever - $basearch + baseurl: https://depot.galaxyproject.org/yum/el/$releasever/$basearch/ + enabled: true + gpgcheck: false + retries: 1 + timeout: 10 + +# Certbot +certbot_virtualenv_package_name: python3-virtualenv +certbot_dns_provider: route53 +certbot_auth_method: --standalone +certbot_domains: "{{ server_names }}" +certbot_post_renewal: | + systemctl restart nginx || true +certbot_share_key_users: + - nginx + +# AWS Credentials for certbot-route53 +aws_cli_credentials: + - access_key: "{{ aws_credentials.certbot.AWS_ACCESS_KEY }}" + secret_key: "{{ aws_credentials.certbot.AWS_SECRET_KEY }}" + homedir: /root + owner: root + group: root + +# rsync to nfs +galaxy_nfs_location: /data/gxkey + +# Nginx +nginx_servers: + - redirect-ssl +nginx_ssl_servers: + - galaxyproject + - telescope-ssl + - galaxy-main + - galaxy-ie-main + - galaxy-test-proxy +nginx_conf_http: + client_max_body_size: 1g + proxy_cache_path: "/tmp/nginx-cache levels=1:2 keys_zone=STATIC:10m inactive=24h max_size=1g" + gzip: "on" + gzip_proxied: any + # The ngx_http_gzip_static_module module allows sending precompressed files with the “.gz” filename extension instead of regular files. + gzip_static: "on" + gzip_http_version: "1.1" + gzip_disable: '"MSIE [1-6]\."' + gzip_vary: "on" + gzip_comp_level: 6 + gzip_types: | + text/plain + text/css + text/xml + text/javascript + application/javascript + application/x-javascript + application/json + application/xml + application/xml+rss + application/xhtml+xml + application/x-font-ttf + application/x-font-opentype + image/png + image/svg+xml + image/x-icon + gzip_buffers: "16 8k" + gzip_min_length: 128 +nginx_enable_default_server: false +nginx_flavor: "" + +# Nginx Letsencrypt bindings +nginx_ssl_role: usegalaxy-eu.certbot +nginx_conf_ssl_certificate: /etc/ssl/certs/fullchain.pem +nginx_conf_ssl_certificate_key: /etc/ssl/user/privkey-nginx.pem + +# Dynmotd +dynmotd_custom: + - name: Condor + command: "condor_q -totals | tail -n 2" + +# TPV Script +tpv_config_dir_name: total_perspective_vortex + +# CVMFS +cvmfs_role: client +galaxy_cvmfs_repos_enabled: config-repo + +galaxy_cvmfs_server_urls: + - domain: galaxyproject.org + urls: + - "http://cvmfs1-ufr0.galaxyproject.eu/cvmfs/@fqrn@" + +# SystemD +galaxy_systemd_mode: "gunicorn" +galaxy_systemd_gunicorns: 7 +galaxy_systemd_gunicorn_workers: 4 +galaxy_systemd_gunicorn_timeout: 600 +galaxy_systemd_handlers: 6 +galaxy_systemd_workflow_schedulers: 3 + +galaxy_systemd_gunicorn_env: "{{ apollo_env }}" +galaxy_systemd_handler_env: "{{ galaxy_systemd_gunicorn_env }}" +galaxy_systemd_workflow_scheduler_env: "{{ galaxy_systemd_gunicorn_env }}" + +galaxy_systemd_memory_limit: 25 +galaxy_systemd_memory_limit_handler: 30 +galaxy_systemd_memory_limit_workflow: 15 + +# gie_proxy +gie_proxy_dir: "{{ galaxy_root }}/gie-proxy/proxy" +gie_proxy_git_version: "v0.0.6" +gie_proxy_setup_nodejs: nodeenv +gie_proxy_virtualenv_command: "{{ conda_prefix }}/envs/_galaxy_/bin/python -m venv --copies" #"{{ pip_virtualenv_command }}" +gie_proxy_nodejs_version: "10.13.0" +gie_proxy_virtualenv: "{{ galaxy_root }}/gie-proxy/venv" +gie_proxy_setup_service: systemd +gie_proxy_sessions_path: "{{ galaxy_mutable_data_dir }}/interactivetools_map.sqlite" +gie_proxy_path_prefix: /interactivetool/ep +gie_proxy_port: 8800 +gie_proxy_verbose: true + +# gxadmin +postgres_user: galaxy +postgres_host: sn05.galaxyproject.eu +postgres_port: 5432 + +# GRT +galaxy_grt_exporter: galaxy +galaxy_grt_uploader: galaxy + +# Influx Notifier +gxadmin_influx_task_notifier: true +gxadmin_influx_task_notifier_db: notifications + +# postgres_pass defined in secret_group_vars/all.yml +gxadmin_commit: main +gxadmin_dir: /opt/gxadmin +gxadmin_bin_dir: /usr/bin +gxadmin_force: true + +# GALAXY +galaxy_group: + name: galaxy + gid: 999 +galaxy_system_group: galaxy +galaxy_log_dir: "/var/log/galaxy" +galaxy_layout: root-dir +galaxy_separate_privileges: true +galaxy_manage_paths: true +galaxy_build_client: false +galaxy_restart_handler_name: Restart Galaxy +galaxy_create_user: true +galaxy_user: + name: galaxy + create_home: true + home: /opt/galaxy + uid: 999 + shell: /bin/bash + +# Galaxy configuration files will be written with these permissions (mode argument to Ansible copy/template module) +galaxy_config_perms: 0644 + +galaxy_root: /opt/galaxy +galaxy_workflow_scheduler_count: "{{ galaxy_systemd_workflow_schedulers }}" +galaxy_home_dir: /opt/galaxy +galaxy_mutable_config_dir: "{{ galaxy_root }}/mutable-config" +galaxy_mutable_data_dir: "{{ galaxy_root }}/mutable-data" +galaxy_shed_tools_dir: "{{ galaxy_root }}/shed_tools" +galaxy_tool_data_path: "{{ galaxy_root }}/tool-data" +__galaxy_shed_tools_dir: "{{ galaxy_shed_tools_dir }}" +galaxy_backup_configfiles: false + +galaxy_server_dir: "{{ galaxy_root }}/server" +galaxy_config_dir: "{{ galaxy_root }}/config" +galaxy_venv_dir: "{{ galaxy_root }}/venv" +galaxy_job_working_directory: "{{ galaxy_config['galaxy']['job_working_directory'] }}" +ucsc_build_sites: + +galaxy_virtualenv_command: "{{ conda_prefix }}/envs/_galaxy_/bin/python -m venv --copies" +#galaxy_virtualenv_python: "python3.6" +galaxy_nonrepro_tools: "{{ galaxy_root }}/custom-tools" +galaxy_nonrepro_commit: master + + +# Custom override +# Our galaxy_tool_dependency_dir is on NFS, and permissions are set in such a +# way that they cannot be changed by the ansible connected user. +galaxy_dirs: + - "{{ galaxy_mutable_data_dir }}" + - "{{ galaxy_mutable_config_dir }}" + - "{{ galaxy_cache_dir }}" + - "{{ galaxy_shed_tools_dir }}" + #- "{{ galaxy_tool_dependency_dir }}" + - "{{ galaxy_file_path }}" + - "{{ galaxy_job_working_directory }}" + - "{{ galaxy_tool_data_path }}" + - "{{ galaxy_nonrepro_tools }}" + - "{{ galaxy_webhook_dir }}" + - "{{ galaxy_tour_dir }}" + - "{{ galaxy_log_dir }}" + - "{{ galaxy_config_dir }}/total_perspective_vortex" + - "{{ tpv_mutable_dir }}" + +galaxy_instance_hostname: usegalaxy.eu +galaxy_config_style: yaml + +galaxy_repo: "https://github.com/usegalaxy-eu/galaxy.git" +galaxy_commit_id: "release_24.1_europe" +galaxy_force_checkout: true # discard any modified files +#galaxy_admin_email_from: 'noreply@usegalaxy.eu' + +galaxy_singularity_images_cvmfs_path: "/cvmfs/singularity.galaxyproject.org/all/" + +galaxy_config: "{{ galaxy_config_hash }}" + +# Galaxy Subdomains +galaxy_themes_ansible_file_path: /scratch/workspace/usegalaxy-eu/playbooks/sn06/files/galaxy/subdomains +galaxy_themes_conf_path: files/galaxy/config/themes_conf.yml +galaxy_themes_default_welcome: https://galaxyproject.org/bare/eu/usegalaxy/main/ +galaxy_themes_welcome_url_prefix: https://usegalaxy-eu.github.io/index- + +galaxy_config_file_src_dir: files/galaxy +galaxy_config_files: + # TODO(bgruening): sync this with cvmfs? can we have ours be just a small additional builds.txt? + - src: "{{ galaxy_config_file_src_dir }}/config/builds.txt" + dest: "{{ galaxy_config['galaxy']['builds_file_path'] }}" + - src: "{{ galaxy_config_file_src_dir }}/config/data_manager_conf.xml" + dest: "{{ galaxy_config['galaxy']['data_manager_config_file'] }}" + - src: "{{ galaxy_config_file_src_dir }}/config/datatypes_conf.xml" + dest: "{{ galaxy_config['galaxy']['datatypes_config_file'] }}" + - src: "{{ galaxy_config_file_src_dir }}/config/dependency_resolvers_conf.xml" + dest: "{{ galaxy_config['galaxy']['dependency_resolvers_config_file'] }}" + - src: "{{ galaxy_config_file_src_dir }}/config/email_domain_blocklist.conf" + dest: "{{ galaxy_config['galaxy']['email_domain_blocklist_file'] }}" + - src: "{{ galaxy_config_file_src_dir }}/config/user_preferences_extra_conf.yml" + dest: "{{ galaxy_config['galaxy']['user_preferences_extra_conf_path'] }}" + - src: "{{ galaxy_config_file_src_dir }}/config/job_resource_params_conf.xml" + dest: "{{ galaxy_config['galaxy']['job_resource_params_file'] }}" + - src: "{{ galaxy_config_file_src_dir }}/config/trs_servers_conf.yml" + dest: "{{ galaxy_config['galaxy']['trs_servers_config_file'] }}" + - src: "{{ galaxy_config_file_src_dir }}/config/themes_conf.yml" + dest: "{{ galaxy_config['galaxy']['themes_config_file'] }}" + # test? Unknown if this works. + - src: "{{ galaxy_config_file_src_dir }}/config/error_report.yml" + dest: "{{ galaxy_config_dir }}/error_report.yml" + - src: "{{ galaxy_config_file_src_dir }}/config/job_metrics_conf.yml" + dest: "{{ galaxy_config['galaxy']['job_metrics_config_file'] }}" + - src: "{{ galaxy_config_file_src_dir }}/config/migrated_tools_conf.xml" + dest: "{{ galaxy_config['galaxy']['migrated_tools_config'] }}" + - src: "{{ galaxy_config_file_src_dir }}/config/tool_data_table_conf.xml" + dest: "{{ galaxy_config_dir }}/tool_data_table_conf.xml" + - src: "{{ galaxy_config_file_src_dir }}/config/tool_sheds_conf.xml" + dest: "{{ galaxy_config['galaxy']['tool_sheds_config_file'] }}" + - src: "{{ galaxy_config_file_src_dir }}/config/ucsc_build_sites.txt" + dest: "{{ galaxy_config['galaxy']['ucsc_build_sites'] }}" + - src: "{{ galaxy_config_file_src_dir }}/config/echo_main_env.xml" + dest: "{{ galaxy_config_dir }}/echo_main_env.xml" + - src: "{{ galaxy_config_file_src_dir }}/tpv/tool_defaults.yml" + dest: "{{ tpv_mutable_dir }}/tool_defaults.yml" + - src: "{{ galaxy_config_file_src_dir }}/tpv/tools.yml" + dest: "{{ tpv_mutable_dir }}/tools.yml" + - src: "{{ galaxy_config_file_src_dir }}/tpv/roles.yml" + dest: "{{ tpv_mutable_dir }}/roles.yml" + - src: "{{ galaxy_config_file_src_dir }}/tpv/interactive_tools.yml" + dest: "{{ tpv_mutable_dir }}/interactive_tools.yml" + - src: "{{ galaxy_config_file_src_dir }}/tpv/users.yml" + dest: "{{ tpv_mutable_dir }}/users.yml" + + #- src: files/galaxy/config/job_resource_params_conf.xml + #dest: "{{ galaxy_config['app:main']['job_resource_params_file'] }}" + #- src: files/galaxy/config/pulsar_stampede_actions.yml + #dest: "{{ galaxy_config_dir }}/pulsar_stampede_actions.yml" + #- src: files/galaxy/config/pulsar_bridges_actions.yml + #dest: "{{ galaxy_config_dir }}/pulsar_bridges_actions.yml" + #- src: files/galaxy/config/pulsar_jetstream.yml + #dest: "{{ galaxy_config_dir }}/pulsar_jetstream.yml" + #- src: files/galaxy/config/pulsar_jetstream_actions.yml + #dest: "{{ galaxy_config_dir }}/pulsar_jetstream_actions.yml" + +galaxy_config_template_src_dir: templates/galaxy +galaxy_config_templates: + - src: "{{ galaxy_config_template_src_dir }}/config/build_sites.yml.j2" + dest: "{{ galaxy_config['galaxy']['build_sites_config_file'] }}" + - src: "{{ galaxy_config_template_src_dir }}/config/global_host_filters.py.j2" + dest: "{{ galaxy_server_dir }}/lib/galaxy/tool_util/toolbox/filters/global_host_filters.py" + - src: "{{ galaxy_config_template_src_dir }}/config/job_conf.yml.j2" + dest: "{{ galaxy_config_dir }}/job_conf.yml" + - src: "{{ galaxy_config_template_src_dir }}/config/container_resolvers_conf.xml.j2" + dest: "{{ galaxy_config_dir }}/container_resolvers_conf.xml" + - src: "{{ galaxy_config_template_src_dir }}/config/user_filters.py.j2" + dest: "{{ galaxy_server_dir }}/lib/galaxy/tool_util/toolbox/filters/user_filters.py" + - src: "{{ galaxy_config_template_src_dir }}/config/nagios_tool_conf.xml" + dest: "{{ galaxy_config_dir }}/nagios_tool_conf.xml" + - src: "{{ galaxy_config_template_src_dir }}/config/oidc_backends_config.xml" + dest: "{{ galaxy_config['galaxy']['oidc_backends_config_file'] }}" + - src: "{{ galaxy_config_template_src_dir }}/config/oidc_config.xml" + dest: "{{ galaxy_config['galaxy']['oidc_config_file'] }}" + - src: "{{ galaxy_config_template_src_dir }}/config/grt.yml.j2" + dest: "{{ galaxy_config_dir }}/grt.yml" + - src: "{{ galaxy_config_template_src_dir }}/config/pulsar_app.yml" + dest: "{{ galaxy_config_dir }}/pulsar_app.yml" + - src: "{{ galaxy_config_template_src_dir }}/config/tool_conf.xml.j2" + dest: "{{ galaxy_config_dir }}/tool_conf.xml" + - src: "{{ galaxy_config_template_src_dir }}/config/galaxy_workflow_scheduler.j2" + dest: "{{ galaxy_config_dir }}/workflow_schedulers_conf.xml" + - src: "{{ galaxy_config_template_src_dir }}/config/file_sources_conf.yml.j2" + dest: "{{ galaxy_config_dir }}/file_sources_conf.yml" + - src: "{{ galaxy_config_template_src_dir }}/config/object_store_conf.xml.j2" + dest: "{{ galaxy_config['galaxy']['object_store_config_file'] }}" + - src: "{{ galaxy_config_file_src_dir }}/tpv/destinations.yml.j2" + dest: "{{ tpv_mutable_dir }}/destinations.yml" + - src: '{{ galaxy_config_template_src_dir }}/config/vault_conf.yml.j2' + dest: '{{ galaxy_config_dir }}/vault_conf.yml' + - src: '{{ galaxy_config_template_src_dir }}/config/file_source_templates.yml.j2' + dest: "{{ galaxy_config['galaxy']['file_source_templates_config_file'] }}" + - src: '{{ galaxy_config_template_src_dir }}/config/object_store_templates.yml.j2' + dest: "{{ galaxy_config['galaxy']['object_store_templates_config_file'] }}" diff --git a/group_vars/sn06/subdomains.yml b/group_vars/sn06/subdomains.yml new file mode 100644 index 000000000..739a4a331 --- /dev/null +++ b/group_vars/sn06/subdomains.yml @@ -0,0 +1,222 @@ +--- +galaxy_themes_subdomains: + - name: assembly + theme: + assembly: + masthead: + color: > + bottom -90px left / 1000px no-repeat url("/static/dist/flying-bird-1.svg"), + bottom -90px left / 1000px no-repeat url("/static/dist/flying-bird-2.svg"), + linear-gradient( 20deg, + rgb(7, 40, 98) 0%, + rgb(69, 122, 184) 48%, + rgba(165, 204, 210, 0.9676562309265136) 74%, + rgb(228, 195, 131) 92%, + rgb(203, 119, 79) 100%) + - name: nanopore + - name: erasmusmc + - name: climate + theme: + climate: + masthead: + color: > + linear-gradient(to right, #3337 0, #3337 340px, transparent 340px), + linear-gradient(to left, #3337 0, #3337 120px, transparent 120px), + linear-gradient(to right, #2171b5 0.00%, + #2171b5 0.83%, #c6dbef 0.83%, #c6dbef 1.65%, #9ecae1 1.65%, #9ecae1 2.48%, #fee0d2 2.48%, + #fee0d2 3.31%, #6baed6 3.31%, #6baed6 4.13%, #9ecae1 4.13%, #9ecae1 4.96%, #08519c 4.96%, + #08519c 5.79%, #08306b 5.79%, #08306b 6.61%, #2171b5 6.61%, #2171b5 7.44%, #4292c6 7.44%, + #4292c6 8.26%, #9ecae1 8.26%, #9ecae1 9.09%, #2171b5 9.09%, #2171b5 9.92%, #4292c6 9.92%, + #4292c6 10.74%, #9ecae1 10.74%, #9ecae1 11.57%, #deebf7 11.57%, #deebf7 12.40%, #9ecae1 12.40%, + #9ecae1 13.22%, #deebf7 13.22%, #deebf7 14.05%, #4292c6 14.05%, #4292c6 14.88%, #08519c 14.88%, + #08519c 15.70%, #deebf7 15.70%, #deebf7 16.53%, #9ecae1 16.53%, #9ecae1 17.36%, #c6dbef 17.36%, + #c6dbef 18.18%, #6baed6 18.18%, #6baed6 19.01%, #4292c6 19.01%, #4292c6 19.83%, #2171b5 19.83%, + #2171b5 20.66%, #deebf7 20.66%, #deebf7 21.49%, #fcbba1 21.49%, #fcbba1 22.31%, #9ecae1 22.31%, + #9ecae1 23.14%, #deebf7 23.14%, #deebf7 23.97%, #9ecae1 23.97%, #9ecae1 24.79%, #deebf7 24.79%, + #deebf7 25.62%, #4292c6 25.62%, #4292c6 26.45%, #deebf7 26.45%, #deebf7 27.27%, #2171b5 27.27%, + #2171b5 28.10%, #fee0d2 28.10%, #fee0d2 28.93%, #fcbba1 28.93%, #fcbba1 29.75%, #08519c 29.75%, + #08519c 30.58%, #9ecae1 30.58%, #9ecae1 31.40%, #4292c6 31.40%, #4292c6 32.23%, #c6dbef 32.23%, + #c6dbef 33.06%, #fee0d2 33.06%, #fee0d2 33.88%, #9ecae1 33.88%, #9ecae1 34.71%, #c6dbef 34.71%, + #c6dbef 35.54%, #2171b5 35.54%, #2171b5 36.36%, #fcbba1 36.36%, #fcbba1 37.19%, #4292c6 37.19%, + #4292c6 38.02%, #c6dbef 38.02%, #c6dbef 38.84%, #4292c6 38.84%, #4292c6 39.67%, #ef3b2c 39.67%, + #ef3b2c 40.50%, #deebf7 40.50%, #deebf7 41.32%, #fee0d2 41.32%, #fee0d2 42.15%, #c6dbef 42.15%, + #c6dbef 42.98%, #08306b 42.98%, #08306b 43.80%, #08519c 43.80%, #08519c 44.63%, #2171b5 44.63%, + #2171b5 45.45%, #fcbba1 45.45%, #fcbba1 46.28%, #c6dbef 46.28%, #c6dbef 47.11%, #fcbba1 47.11%, + #fcbba1 47.93%, #deebf7 47.93%, #deebf7 48.76%, #fcbba1 48.76%, #fcbba1 49.59%, #fc9272 49.59%, + #fc9272 50.41%, #fee0d2 50.41%, #fee0d2 51.24%, #9ecae1 51.24%, #9ecae1 52.07%, #fcbba1 52.07%, + #fcbba1 52.89%, #6baed6 52.89%, #6baed6 53.72%, #4292c6 53.72%, #4292c6 54.55%, #08306b 54.55%, + #08306b 55.37%, #fee0d2 55.37%, #fee0d2 56.20%, #c6dbef 56.20%, #c6dbef 57.02%, #fcbba1 57.02%, + #fcbba1 57.85%, #deebf7 57.85%, #deebf7 58.68%, #fcbba1 58.68%, #fcbba1 59.50%, #08519c 59.50%, + #08519c 60.33%, #9ecae1 60.33%, #9ecae1 61.16%, #4292c6 61.16%, #4292c6 61.98%, #deebf7 61.98%, + #deebf7 62.81%, #fcbba1 62.81%, #fcbba1 63.64%, #9ecae1 63.64%, #9ecae1 64.46%, #6baed6 64.46%, + #6baed6 65.29%, #deebf7 65.29%, #deebf7 66.12%, #6baed6 66.12%, #6baed6 66.94%, #c6dbef 66.94%, + #c6dbef 67.77%, #fcbba1 67.77%, #fcbba1 68.60%, #deebf7 68.60%, #deebf7 69.42%, #fee0d2 69.42%, + #fee0d2 70.25%, #6baed6 70.25%, #6baed6 71.07%, #4292c6 71.07%, #4292c6 71.90%, #c6dbef 71.90%, + #c6dbef 72.73%, #fcbba1 72.73%, #fcbba1 73.55%, #9ecae1 73.55%, #9ecae1 74.38%, #2171b5 74.38%, + #2171b5 75.21%, #9ecae1 75.21%, #9ecae1 76.03%, #2171b5 76.03%, #2171b5 76.86%, #fc9272 76.86%, + #fc9272 77.69%, #ef3b2c 77.69%, #ef3b2c 78.51%, #c6dbef 78.51%, #c6dbef 79.34%, #fb6a4a 79.34%, + #fb6a4a 80.17%, #deebf7 80.17%, #deebf7 80.99%, #cb181d 80.99%, #cb181d 81.82%, #fcbba1 81.82%, + #fcbba1 82.64%, #08519c 82.64%, #08519c 83.47%, #fcbba1 83.47%, #fcbba1 84.30%, #fc9272 84.30%, + #fc9272 85.12%, #ef3b2c 85.12%, #ef3b2c 85.95%, #cb181d 85.95%, #cb181d 86.78%, #fcbba1 86.78%, + #fcbba1 87.60%, #ef3b2c 87.60%, #ef3b2c 88.43%, #fb6a4a 88.43%, #fb6a4a 89.26%, #fcbba1 89.26%, + #fcbba1 90.08%, #ef3b2c 90.08%, #ef3b2c 90.91%, #cb181d 90.91%, #cb181d 91.74%, #ef3b2c 91.74%, + #ef3b2c 92.56%, #fc9272 92.56%, #fc9272 93.39%, #6baed6 93.39%, #6baed6 94.21%, #ef3b2c 94.21%, + #ef3b2c 95.04%, #fc9272 95.04%, #fc9272 95.87%, #fee0d2 95.87%, #fee0d2 96.69%, #67000d 96.69%, + #67000d 97.52%, #cb181d 97.52%, #cb181d 98.35%, #ef3b2c 98.35%, #ef3b2c 99.17%, #67000d 99.17%, + #67000d 100.00%) + link: + color: "#3337" + hover: "#3339" + active: "#333e" + - name: hicexplorer + theme: + hicexplorer: + masthead: + color: > + linear-gradient(to right, #3337 0, #3337 285px, transparent 285px), + linear-gradient(to left, #3337 0, #3337 120px, transparent 120px), + left / 340px url("/static/dist/hicexplorer.png") + link: + color: "#3337" + hover: "#3339" + active: "#333e" + - name: annotation + theme: + annotation: + masthead: + color: > + linear-gradient(to right, #3337 0, #3337 365px, transparent 365px), + linear-gradient(to left, #3337 0, #3337 120px, transparent 120px), + left / 23% url("/static/dist/annotation.png") + link: + color: "#3337" + hover: "#3339" + active: "#333e" + - name: metabolomics + - name: metagenomics + - name: microbiome + - name: microgalaxy + - name: rna + - name: graphclust + - name: ecology + theme: + ecology: + masthead: + color: > + linear-gradient(to right, #3337 0, #3337 340px, transparent 340px), + linear-gradient(to left, #3337 0, #3337 120px, transparent 120px), + linear-gradient(to right, #2171b5 0.00%, + #2171b5 0.83%, #c6dbef 0.83%, #c6dbef 1.65%, #9ecae1 1.65%, #9ecae1 2.48%, #fee0d2 2.48%, + #fee0d2 3.31%, #6baed6 3.31%, #6baed6 4.13%, #9ecae1 4.13%, #9ecae1 4.96%, #08519c 4.96%, + #08519c 5.79%, #08306b 5.79%, #08306b 6.61%, #2171b5 6.61%, #2171b5 7.44%, #4292c6 7.44%, + #4292c6 8.26%, #9ecae1 8.26%, #9ecae1 9.09%, #2171b5 9.09%, #2171b5 9.92%, #4292c6 9.92%, + #4292c6 10.74%, #9ecae1 10.74%, #9ecae1 11.57%, #deebf7 11.57%, #deebf7 12.40%, #9ecae1 12.40%, + #9ecae1 13.22%, #deebf7 13.22%, #deebf7 14.05%, #4292c6 14.05%, #4292c6 14.88%, #08519c 14.88%, + #08519c 15.70%, #deebf7 15.70%, #deebf7 16.53%, #9ecae1 16.53%, #9ecae1 17.36%, #c6dbef 17.36%, + #c6dbef 18.18%, #6baed6 18.18%, #6baed6 19.01%, #4292c6 19.01%, #4292c6 19.83%, #2171b5 19.83%, + #2171b5 20.66%, #deebf7 20.66%, #deebf7 21.49%, #fcbba1 21.49%, #fcbba1 22.31%, #9ecae1 22.31%, + #9ecae1 23.14%, #deebf7 23.14%, #deebf7 23.97%, #9ecae1 23.97%, #9ecae1 24.79%, #deebf7 24.79%, + #deebf7 25.62%, #4292c6 25.62%, #4292c6 26.45%, #deebf7 26.45%, #deebf7 27.27%, #2171b5 27.27%, + #2171b5 28.10%, #fee0d2 28.10%, #fee0d2 28.93%, #fcbba1 28.93%, #fcbba1 29.75%, #08519c 29.75%, + #08519c 30.58%, #9ecae1 30.58%, #9ecae1 31.40%, #4292c6 31.40%, #4292c6 32.23%, #c6dbef 32.23%, + #c6dbef 33.06%, #fee0d2 33.06%, #fee0d2 33.88%, #9ecae1 33.88%, #9ecae1 34.71%, #c6dbef 34.71%, + #c6dbef 35.54%, #2171b5 35.54%, #2171b5 36.36%, #fcbba1 36.36%, #fcbba1 37.19%, #4292c6 37.19%, + #4292c6 38.02%, #c6dbef 38.02%, #c6dbef 38.84%, #4292c6 38.84%, #4292c6 39.67%, #ef3b2c 39.67%, + #ef3b2c 40.50%, #deebf7 40.50%, #deebf7 41.32%, #fee0d2 41.32%, #fee0d2 42.15%, #c6dbef 42.15%, + #c6dbef 42.98%, #08306b 42.98%, #08306b 43.80%, #08519c 43.80%, #08519c 44.63%, #2171b5 44.63%, + #2171b5 45.45%, #fcbba1 45.45%, #fcbba1 46.28%, #c6dbef 46.28%, #c6dbef 47.11%, #fcbba1 47.11%, + #fcbba1 47.93%, #deebf7 47.93%, #deebf7 48.76%, #fcbba1 48.76%, #fcbba1 49.59%, #fc9272 49.59%, + #fc9272 50.41%, #fee0d2 50.41%, #fee0d2 51.24%, #9ecae1 51.24%, #9ecae1 52.07%, #fcbba1 52.07%, + #fcbba1 52.89%, #6baed6 52.89%, #6baed6 53.72%, #4292c6 53.72%, #4292c6 54.55%, #08306b 54.55%, + #08306b 55.37%, #fee0d2 55.37%, #fee0d2 56.20%, #c6dbef 56.20%, #c6dbef 57.02%, #fcbba1 57.02%, + #fcbba1 57.85%, #deebf7 57.85%, #deebf7 58.68%, #fcbba1 58.68%, #fcbba1 59.50%, #08519c 59.50%, + #08519c 60.33%, #9ecae1 60.33%, #9ecae1 61.16%, #4292c6 61.16%, #4292c6 61.98%, #deebf7 61.98%, + #deebf7 62.81%, #fcbba1 62.81%, #fcbba1 63.64%, #9ecae1 63.64%, #9ecae1 64.46%, #6baed6 64.46%, + #6baed6 65.29%, #deebf7 65.29%, #deebf7 66.12%, #6baed6 66.12%, #6baed6 66.94%, #c6dbef 66.94%, + #c6dbef 67.77%, #fcbba1 67.77%, #fcbba1 68.60%, #deebf7 68.60%, #deebf7 69.42%, #fee0d2 69.42%, + #fee0d2 70.25%, #6baed6 70.25%, #6baed6 71.07%, #4292c6 71.07%, #4292c6 71.90%, #c6dbef 71.90%, + #c6dbef 72.73%, #fcbba1 72.73%, #fcbba1 73.55%, #9ecae1 73.55%, #9ecae1 74.38%, #2171b5 74.38%, + #2171b5 75.21%, #9ecae1 75.21%, #9ecae1 76.03%, #2171b5 76.03%, #2171b5 76.86%, #fc9272 76.86%, + #fc9272 77.69%, #ef3b2c 77.69%, #ef3b2c 78.51%, #c6dbef 78.51%, #c6dbef 79.34%, #fb6a4a 79.34%, + #fb6a4a 80.17%, #deebf7 80.17%, #deebf7 80.99%, #cb181d 80.99%, #cb181d 81.82%, #fcbba1 81.82%, + #fcbba1 82.64%, #08519c 82.64%, #08519c 83.47%, #fcbba1 83.47%, #fcbba1 84.30%, #fc9272 84.30%, + #fc9272 85.12%, #ef3b2c 85.12%, #ef3b2c 85.95%, #cb181d 85.95%, #cb181d 86.78%, #fcbba1 86.78%, + #fcbba1 87.60%, #ef3b2c 87.60%, #ef3b2c 88.43%, #fb6a4a 88.43%, #fb6a4a 89.26%, #fcbba1 89.26%, + #fcbba1 90.08%, #ef3b2c 90.08%, #ef3b2c 90.91%, #cb181d 90.91%, #cb181d 91.74%, #ef3b2c 91.74%, + #ef3b2c 92.56%, #fc9272 92.56%, #fc9272 93.39%, #6baed6 93.39%, #6baed6 94.21%, #ef3b2c 94.21%, + #ef3b2c 95.04%, #fc9272 95.04%, #fc9272 95.87%, #fee0d2 95.87%, #fee0d2 96.69%, #67000d 96.69%, + #67000d 97.52%, #cb181d 97.52%, #cb181d 98.35%, #ef3b2c 98.35%, #ef3b2c 99.17%, #67000d 99.17%, + #67000d 100.00%) + link: + color: "#3337" + hover: "#3339" + active: "#333e" + - name: proteomics + - name: clipseq + - name: cheminformatics + - name: imaging + theme: + imaging: + masthead: + color: > + linear-gradient(90deg, + rgb(0, 0, 0) 0%, + rgb(0, 69, 227) 17%, + rgb(9, 121, 33) 30%, + rgb(180, 170, 15) 70%, + rgb(193, 35, 0) 79%, + rgb(0, 0, 0) 100%) + - name: test + - name: beta + - name: streetscience + - name: singlecell + theme: + singlecell: + masthead: + color: "#530080" + - name: humancellatlas + - name: ml + - name: live + theme: + live: + masthead: + color: > + linear-gradient(33deg, rgba(131,58,180,1) 0%, + rgba(253,29,29,1) 25%, rgba(252,176,69,1) 50%, + rgba(253,29,29,1) 75%, rgba(131,58,180,1) 100%) + - name: plants + theme: + plants: + masthead: + color: > + linear-gradient(90deg, + #1a5d1a 0%, + #369c36 50%, + rgb(29 95 28) 100%) + - name: virology + theme: + virology: + masthead: + color: > + linear-gradient(50deg, + hsl(240deg 100% 20%) 0%, + hsl(234deg 95% 23%) 13%, + hsl(227deg 90% 26%) 26%, + hsl(220deg 85% 29%) 38%, + hsl(213deg 79% 32%) 52%, + hsl(207deg 74% 35%) 66%, + hsl(200deg 69% 38%) 82%, + hsl(194deg 64% 42%) 100%) + - name: lite + - name: covid19 + - name: africa + - name: india + - name: spatialomics + - name: materials + - name: phage + - name: earth-system + - name: cancer + - name: aqua + - name: eirene + + diff --git a/requirements.yaml b/requirements.yaml index d1eb9443f..ce4bc3662 100644 --- a/requirements.yaml +++ b/requirements.yaml @@ -58,7 +58,7 @@ roles: version: 0.14.1 - name: galaxyproject.galaxy src: https://github.com/galaxyproject/ansible-galaxy - version: 0.10.18 + version: 0.11.1 - name: galaxyproject.cvmfs src: https://github.com/usegalaxy-eu/ansible-cvmfs version: master diff --git a/sn06.yml b/sn06.yml index f7a8cc3e8..6bc98085b 100644 --- a/sn06.yml +++ b/sn06.yml @@ -48,7 +48,6 @@ - "*.eirene.usegalaxy.eu" - "*.ep.interactivetool.eirene.usegalaxy.eu" vars_files: - - group_vars/sn06.yml - group_vars/tiaas.yml # All of the training infrastructure - group_vars/gxconfig.yml # The base galaxy configuration - group_vars/toolbox.yml # User controlled toolbox @@ -186,7 +185,6 @@ galaxy_manage_static_setup: false galaxy_manage_mutable_setup: false galaxy_manage_database: false - galaxy_manage_themes: false galaxy_manage_subdomain_static: false galaxy_fetch_dependencies: false galaxy_build_client: false @@ -237,7 +235,6 @@ galaxy_manage_static_setup: true galaxy_manage_mutable_setup: true galaxy_manage_database: true - galaxy_manage_themes: true galaxy_manage_subdomain_static: true galaxy_manage_host_filters: false # test when themes work galaxy_manage_systemd: false # switch to gravity(?) From bc2bb14049cceeddcca2ed0a76955e9a8f4e9f1f Mon Sep 17 00:00:00 2001 From: Mira Kuntz Date: Mon, 11 Nov 2024 10:30:27 +0100 Subject: [PATCH 2/3] lint --- group_vars/sn06/subdomains.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/group_vars/sn06/subdomains.yml b/group_vars/sn06/subdomains.yml index 739a4a331..b2614575b 100644 --- a/group_vars/sn06/subdomains.yml +++ b/group_vars/sn06/subdomains.yml @@ -219,4 +219,3 @@ galaxy_themes_subdomains: - name: aqua - name: eirene - From 83dfc0902da8a301ad8c301cfd431ef53f82aa86 Mon Sep 17 00:00:00 2001 From: Mira Kuntz Date: Mon, 11 Nov 2024 11:55:07 +0100 Subject: [PATCH 3/3] remove group_vars/sn06.yml --- group_vars/sn06.yml | 435 --------------------------------- group_vars/sn06/subdomains.yml | 1 - 2 files changed, 436 deletions(-) delete mode 100644 group_vars/sn06.yml diff --git a/group_vars/sn06.yml b/group_vars/sn06.yml deleted file mode 100644 index 226bda691..000000000 --- a/group_vars/sn06.yml +++ /dev/null @@ -1,435 +0,0 @@ ---- -# packages -software_groups_to_install: - - admin - - debug - - editors - - pdf_export_deps - - services - - terminals - - utils - -# Docker -docker_users: - - galaxy - -# Autofs -autofs_service.install: true -autofs_service.enable: true -nfs_kernel_tuning: true - -autofs_mount_points: - - data - - gxtest - - gxkey - - jwd - - usrlocal - -# Miniconda role variables (galaxyproject.miniconda) -conda_prefix: /opt/miniconda - -# fs-maintenance -fsm_maintenance_dir: "/data/dnb01/maintenance" -fsm_cron_tasks: - docker: - enable: true - name: "Docker clean up" - minute: 30 - hour: 2 - dom: "*" - month: "*" - dow: "*" - job: ". {{ galaxy_root }}/.bashrc && docker system prune -f > /dev/null" - user: "{{ fsm_galaxy_user.username }}" - gxadmin: - enable: true - name: "Gxadmin Galaxy clean up" - minute: 0 - hour: 0 - dom: "*/2" - month: "*" - dow: "*" - job: "{{ custom_telegraf_env }} /usr/bin/gxadmin galaxy cleanup 60" - user: "{{ fsm_galaxy_user.username }}" - -# TIaaS -tiaas_virtualenv_python: "python3.8" - -# Telegraf -telegraf_agent_hostname: "{{ hostname }}" -telegraf_agent_version: 1.17.2 -custom_telegraf_env: "/usr/bin/env GDPR_MODE=1 PGUSER={{ galaxy_user.name }} PGHOST={{ postgres_host }} GALAXY_ROOT={{ galaxy_server_dir }} GALAXY_CONFIG_FILE={{ galaxy_config_file }} GALAXY_LOG_DIR={{ galaxy_log_dir }} GXADMIN_PYTHON={{ galaxy_venv_dir }}/bin/python" -telegraf_plugins_extra: - listen_galaxy_routes: - plugin: "statsd" - config: - - service_address = ":8125" - - percentiles = [90] - - metric_separator = "." - - allowed_pending_messages = 10000 - - percentile_limit = 100 - - # Some custom galaxy monitoring stuff that can only run on the Galaxy server - galaxy_lastlog: - plugin: "exec" - config: - - commands = ["{{ custom_telegraf_env }} /usr/bin/gxadmin gunicorn lastlog"] - - timeout = "15s" - - data_format = "influx" - - interval = "15s" - galaxy_active_users: - plugin: "exec" - config: - - commands = ["/usr/bin/gxadmin gunicorn active-users"] - - timeout = "90s" - - data_format = "influx" - - interval = "5m" - -# Custom pip installer -pip_venv_path: "{{ galaxy_venv_dir }}" -pip_install_dependencies: - # celery and flower - - redis - - flower - # phdcomics - - beautifulsoup4 - # Used by code_files for apollo - - biopython - - bcbio-gff - # Needed for tool watching - - watchdog - # Needed gxadmin graphs - - data_hacks - # used by reports - - WeasyPrint - - nbconvert - - gitlab-arc-fs - # Needed for usegalaxy-eu.vgcn-monitoring Telegraf role - - pyyaml - - GitPython - - python-openstackclient - # WallE - - tqdm # progress bar, has no dependencies - -yum_exclude_repos: - - condor* - - npm* - -all_yum_repositories: - - name: galaxy_gpel - description: Galaxy Packages for Enterprise Linux $releasever - $basearch - baseurl: https://depot.galaxyproject.org/yum/el/$releasever/$basearch/ - enabled: true - gpgcheck: false - retries: 1 - timeout: 10 - -# Certbot -certbot_virtualenv_package_name: python3-virtualenv -certbot_dns_provider: route53 -certbot_auth_method: --standalone -certbot_domains: "{{ server_names }}" -certbot_post_renewal: | - systemctl restart nginx || true -certbot_share_key_users: - - nginx - -# AWS Credentials for certbot-route53 -aws_cli_credentials: - - access_key: "{{ aws_credentials.certbot.AWS_ACCESS_KEY }}" - secret_key: "{{ aws_credentials.certbot.AWS_SECRET_KEY }}" - homedir: /root - owner: root - group: root - -# rsync to nfs -galaxy_nfs_location: /data/gxkey - -# Nginx -nginx_servers: - - redirect-ssl -nginx_ssl_servers: - - galaxyproject - - telescope-ssl - - galaxy-main - - galaxy-ie-main - - galaxy-test-proxy -nginx_conf_http: - client_max_body_size: 1g - proxy_cache_path: "/tmp/nginx-cache levels=1:2 keys_zone=STATIC:10m inactive=24h max_size=1g" - gzip: "on" - gzip_proxied: any - # The ngx_http_gzip_static_module module allows sending precompressed files with the “.gz” filename extension instead of regular files. - gzip_static: "on" - gzip_http_version: "1.1" - gzip_disable: '"MSIE [1-6]\."' - gzip_vary: "on" - gzip_comp_level: 6 - gzip_types: | - text/plain - text/css - text/xml - text/javascript - application/javascript - application/x-javascript - application/json - application/xml - application/xml+rss - application/xhtml+xml - application/x-font-ttf - application/x-font-opentype - image/png - image/svg+xml - image/x-icon - gzip_buffers: "16 8k" - gzip_min_length: 128 -nginx_enable_default_server: false -nginx_flavor: "" - -# Nginx Letsencrypt bindings -nginx_ssl_role: usegalaxy-eu.certbot -nginx_conf_ssl_certificate: /etc/ssl/certs/fullchain.pem -nginx_conf_ssl_certificate_key: /etc/ssl/user/privkey-nginx.pem - -# Dynmotd -dynmotd_custom: - - name: Condor - command: "condor_q -totals | tail -n 2" - -# TPV Script -tpv_config_dir_name: total_perspective_vortex - -# CVMFS -cvmfs_role: client -galaxy_cvmfs_repos_enabled: config-repo - -galaxy_cvmfs_server_urls: - - domain: galaxyproject.org - urls: - - "http://cvmfs1-ufr0.galaxyproject.eu/cvmfs/@fqrn@" - -# SystemD -galaxy_systemd_mode: "gunicorn" -galaxy_systemd_gunicorns: 7 -galaxy_systemd_gunicorn_workers: 4 -galaxy_systemd_gunicorn_timeout: 600 -galaxy_systemd_handlers: 6 -galaxy_systemd_workflow_schedulers: 3 - -galaxy_systemd_gunicorn_env: "{{ apollo_env }}" -galaxy_systemd_handler_env: "{{ galaxy_systemd_gunicorn_env }}" -galaxy_systemd_workflow_scheduler_env: "{{ galaxy_systemd_gunicorn_env }}" - -galaxy_systemd_memory_limit: 25 -galaxy_systemd_memory_limit_handler: 30 -galaxy_systemd_memory_limit_workflow: 15 - -# gie_proxy -gie_proxy_dir: "{{ galaxy_root }}/gie-proxy/proxy" -gie_proxy_git_version: "v0.0.6" -gie_proxy_setup_nodejs: nodeenv -gie_proxy_virtualenv_command: "{{ conda_prefix }}/envs/_galaxy_/bin/python -m venv --copies" #"{{ pip_virtualenv_command }}" -gie_proxy_nodejs_version: "10.13.0" -gie_proxy_virtualenv: "{{ galaxy_root }}/gie-proxy/venv" -gie_proxy_setup_service: systemd -gie_proxy_sessions_path: "{{ galaxy_mutable_data_dir }}/interactivetools_map.sqlite" -gie_proxy_path_prefix: /interactivetool/ep -gie_proxy_port: 8800 -gie_proxy_verbose: true - -# gxadmin -postgres_user: galaxy -postgres_host: sn05.galaxyproject.eu -postgres_port: 5432 - -# GRT -galaxy_grt_exporter: galaxy -galaxy_grt_uploader: galaxy - -# Influx Notifier -gxadmin_influx_task_notifier: true -gxadmin_influx_task_notifier_db: notifications - -# postgres_pass defined in secret_group_vars/all.yml -gxadmin_commit: main -gxadmin_dir: /opt/gxadmin -gxadmin_bin_dir: /usr/bin -gxadmin_force: true - -# GALAXY -galaxy_group: - name: galaxy - gid: 999 -galaxy_system_group: galaxy -galaxy_log_dir: "/var/log/galaxy" -galaxy_layout: root-dir -galaxy_separate_privileges: true -galaxy_manage_paths: true -galaxy_build_client: false -galaxy_restart_handler_name: Restart Galaxy -galaxy_create_user: true -galaxy_user: - name: galaxy - create_home: true - home: /opt/galaxy - uid: 999 - shell: /bin/bash - -# Galaxy configuration files will be written with these permissions (mode argument to Ansible copy/template module) -galaxy_config_perms: 0644 - -galaxy_root: /opt/galaxy -galaxy_workflow_scheduler_count: "{{ galaxy_systemd_workflow_schedulers }}" -galaxy_home_dir: /opt/galaxy -galaxy_mutable_config_dir: "{{ galaxy_root }}/mutable-config" -galaxy_mutable_data_dir: "{{ galaxy_root }}/mutable-data" -galaxy_shed_tools_dir: "{{ galaxy_root }}/shed_tools" -galaxy_tool_data_path: "{{ galaxy_root }}/tool-data" -__galaxy_shed_tools_dir: "{{ galaxy_shed_tools_dir }}" -galaxy_backup_configfiles: false - -galaxy_server_dir: "{{ galaxy_root }}/server" -galaxy_config_dir: "{{ galaxy_root }}/config" -galaxy_venv_dir: "{{ galaxy_root }}/venv" -galaxy_job_working_directory: "{{ galaxy_config['galaxy']['job_working_directory'] }}" -ucsc_build_sites: - -galaxy_virtualenv_command: "{{ conda_prefix }}/envs/_galaxy_/bin/python -m venv --copies" -#galaxy_virtualenv_python: "python3.6" -galaxy_nonrepro_tools: "{{ galaxy_root }}/custom-tools" -galaxy_nonrepro_commit: master - - -# Custom override -# Our galaxy_tool_dependency_dir is on NFS, and permissions are set in such a -# way that they cannot be changed by the ansible connected user. -galaxy_dirs: - - "{{ galaxy_mutable_data_dir }}" - - "{{ galaxy_mutable_config_dir }}" - - "{{ galaxy_cache_dir }}" - - "{{ galaxy_shed_tools_dir }}" - #- "{{ galaxy_tool_dependency_dir }}" - - "{{ galaxy_file_path }}" - - "{{ galaxy_job_working_directory }}" - - "{{ galaxy_tool_data_path }}" - - "{{ galaxy_nonrepro_tools }}" - - "{{ galaxy_webhook_dir }}" - - "{{ galaxy_tour_dir }}" - - "{{ galaxy_log_dir }}" - - "{{ galaxy_config_dir }}/total_perspective_vortex" - - "{{ tpv_mutable_dir }}" - -galaxy_instance_hostname: usegalaxy.eu -galaxy_config_style: yaml - -galaxy_repo: "https://github.com/usegalaxy-eu/galaxy.git" -galaxy_commit_id: "release_24.1_europe" -galaxy_force_checkout: true # discard any modified files -#galaxy_admin_email_from: 'noreply@usegalaxy.eu' - -galaxy_singularity_images_cvmfs_path: "/cvmfs/singularity.galaxyproject.org/all/" - -galaxy_config: "{{ galaxy_config_hash }}" - -# Galaxy Subdomains -galaxy_themes_ansible_file_path: /scratch/workspace/usegalaxy-eu/playbooks/sn06/files/galaxy/subdomains -galaxy_themes_conf_path: files/galaxy/config/themes_conf.yml -galaxy_themes_default_welcome: https://galaxyproject.org/bare/eu/usegalaxy/main/ -galaxy_themes_welcome_url_prefix: https://usegalaxy-eu.github.io/index- - -galaxy_config_file_src_dir: files/galaxy -galaxy_config_files: - # TODO(bgruening): sync this with cvmfs? can we have ours be just a small additional builds.txt? - - src: "{{ galaxy_config_file_src_dir }}/config/builds.txt" - dest: "{{ galaxy_config['galaxy']['builds_file_path'] }}" - - src: "{{ galaxy_config_file_src_dir }}/config/data_manager_conf.xml" - dest: "{{ galaxy_config['galaxy']['data_manager_config_file'] }}" - - src: "{{ galaxy_config_file_src_dir }}/config/datatypes_conf.xml" - dest: "{{ galaxy_config['galaxy']['datatypes_config_file'] }}" - - src: "{{ galaxy_config_file_src_dir }}/config/dependency_resolvers_conf.xml" - dest: "{{ galaxy_config['galaxy']['dependency_resolvers_config_file'] }}" - - src: "{{ galaxy_config_file_src_dir }}/config/email_domain_blocklist.conf" - dest: "{{ galaxy_config['galaxy']['email_domain_blocklist_file'] }}" - - src: "{{ galaxy_config_file_src_dir }}/config/user_preferences_extra_conf.yml" - dest: "{{ galaxy_config['galaxy']['user_preferences_extra_conf_path'] }}" - - src: "{{ galaxy_config_file_src_dir }}/config/job_resource_params_conf.xml" - dest: "{{ galaxy_config['galaxy']['job_resource_params_file'] }}" - - src: "{{ galaxy_config_file_src_dir }}/config/trs_servers_conf.yml" - dest: "{{ galaxy_config['galaxy']['trs_servers_config_file'] }}" - - src: "{{ galaxy_config_file_src_dir }}/config/themes_conf.yml" - dest: "{{ galaxy_config['galaxy']['themes_config_file'] }}" - # test? Unknown if this works. - - src: "{{ galaxy_config_file_src_dir }}/config/error_report.yml" - dest: "{{ galaxy_config_dir }}/error_report.yml" - - src: "{{ galaxy_config_file_src_dir }}/config/job_metrics_conf.yml" - dest: "{{ galaxy_config['galaxy']['job_metrics_config_file'] }}" - - src: "{{ galaxy_config_file_src_dir }}/config/migrated_tools_conf.xml" - dest: "{{ galaxy_config['galaxy']['migrated_tools_config'] }}" - - src: "{{ galaxy_config_file_src_dir }}/config/tool_data_table_conf.xml" - dest: "{{ galaxy_config_dir }}/tool_data_table_conf.xml" - - src: "{{ galaxy_config_file_src_dir }}/config/tool_sheds_conf.xml" - dest: "{{ galaxy_config['galaxy']['tool_sheds_config_file'] }}" - - src: "{{ galaxy_config_file_src_dir }}/config/ucsc_build_sites.txt" - dest: "{{ galaxy_config['galaxy']['ucsc_build_sites'] }}" - - src: "{{ galaxy_config_file_src_dir }}/config/echo_main_env.xml" - dest: "{{ galaxy_config_dir }}/echo_main_env.xml" - - src: "{{ galaxy_config_file_src_dir }}/tpv/tool_defaults.yml" - dest: "{{ tpv_mutable_dir }}/tool_defaults.yml" - - src: "{{ galaxy_config_file_src_dir }}/tpv/tools.yml" - dest: "{{ tpv_mutable_dir }}/tools.yml" - - src: "{{ galaxy_config_file_src_dir }}/tpv/roles.yml" - dest: "{{ tpv_mutable_dir }}/roles.yml" - - src: "{{ galaxy_config_file_src_dir }}/tpv/interactive_tools.yml" - dest: "{{ tpv_mutable_dir }}/interactive_tools.yml" - - src: "{{ galaxy_config_file_src_dir }}/tpv/users.yml" - dest: "{{ tpv_mutable_dir }}/users.yml" - - #- src: files/galaxy/config/job_resource_params_conf.xml - #dest: "{{ galaxy_config['app:main']['job_resource_params_file'] }}" - #- src: files/galaxy/config/pulsar_stampede_actions.yml - #dest: "{{ galaxy_config_dir }}/pulsar_stampede_actions.yml" - #- src: files/galaxy/config/pulsar_bridges_actions.yml - #dest: "{{ galaxy_config_dir }}/pulsar_bridges_actions.yml" - #- src: files/galaxy/config/pulsar_jetstream.yml - #dest: "{{ galaxy_config_dir }}/pulsar_jetstream.yml" - #- src: files/galaxy/config/pulsar_jetstream_actions.yml - #dest: "{{ galaxy_config_dir }}/pulsar_jetstream_actions.yml" - -galaxy_config_template_src_dir: templates/galaxy -galaxy_config_templates: - - src: "{{ galaxy_config_template_src_dir }}/config/build_sites.yml.j2" - dest: "{{ galaxy_config['galaxy']['build_sites_config_file'] }}" - - src: "{{ galaxy_config_template_src_dir }}/config/global_host_filters.py.j2" - dest: "{{ galaxy_server_dir }}/lib/galaxy/tool_util/toolbox/filters/global_host_filters.py" - - src: "{{ galaxy_config_template_src_dir }}/config/job_conf.yml.j2" - dest: "{{ galaxy_config_dir }}/job_conf.yml" - - src: "{{ galaxy_config_template_src_dir }}/config/container_resolvers_conf.xml.j2" - dest: "{{ galaxy_config_dir }}/container_resolvers_conf.xml" - - src: "{{ galaxy_config_template_src_dir }}/config/user_filters.py.j2" - dest: "{{ galaxy_server_dir }}/lib/galaxy/tool_util/toolbox/filters/user_filters.py" - - src: "{{ galaxy_config_template_src_dir }}/config/nagios_tool_conf.xml" - dest: "{{ galaxy_config_dir }}/nagios_tool_conf.xml" - - src: "{{ galaxy_config_template_src_dir }}/config/oidc_backends_config.xml" - dest: "{{ galaxy_config['galaxy']['oidc_backends_config_file'] }}" - - src: "{{ galaxy_config_template_src_dir }}/config/oidc_config.xml" - dest: "{{ galaxy_config['galaxy']['oidc_config_file'] }}" - - src: "{{ galaxy_config_template_src_dir }}/config/grt.yml.j2" - dest: "{{ galaxy_config_dir }}/grt.yml" - - src: "{{ galaxy_config_template_src_dir }}/config/pulsar_app.yml" - dest: "{{ galaxy_config_dir }}/pulsar_app.yml" - - src: "{{ galaxy_config_template_src_dir }}/config/tool_conf.xml.j2" - dest: "{{ galaxy_config_dir }}/tool_conf.xml" - - src: "{{ galaxy_config_template_src_dir }}/config/galaxy_workflow_scheduler.j2" - dest: "{{ galaxy_config_dir }}/workflow_schedulers_conf.xml" - - src: "{{ galaxy_config_template_src_dir }}/config/file_sources_conf.yml.j2" - dest: "{{ galaxy_config_dir }}/file_sources_conf.yml" - - src: "{{ galaxy_config_template_src_dir }}/config/object_store_conf.xml.j2" - dest: "{{ galaxy_config['galaxy']['object_store_config_file'] }}" - - src: "{{ galaxy_config_file_src_dir }}/tpv/destinations.yml.j2" - dest: "{{ tpv_mutable_dir }}/destinations.yml" - - src: '{{ galaxy_config_template_src_dir }}/config/vault_conf.yml.j2' - dest: '{{ galaxy_config_dir }}/vault_conf.yml' - - src: '{{ galaxy_config_template_src_dir }}/config/file_source_templates.yml.j2' - dest: "{{ galaxy_config['galaxy']['file_source_templates_config_file'] }}" - - src: '{{ galaxy_config_template_src_dir }}/config/object_store_templates.yml.j2' - dest: "{{ galaxy_config['galaxy']['object_store_templates_config_file'] }}" diff --git a/group_vars/sn06/subdomains.yml b/group_vars/sn06/subdomains.yml index b2614575b..63f09d5ee 100644 --- a/group_vars/sn06/subdomains.yml +++ b/group_vars/sn06/subdomains.yml @@ -218,4 +218,3 @@ galaxy_themes_subdomains: - name: cancer - name: aqua - name: eirene -