From d4f36c410e14bec8bf5a42ea4ff20e2ae4db5897 Mon Sep 17 00:00:00 2001 From: Ross Lazarus Date: Sat, 21 Sep 2024 15:56:41 +1000 Subject: [PATCH] JBrowse2 update to 2.15.4 (#1504) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * adding first tested and working generated tool from https://github.com/fubar2/nftoolmaker It actually does work. Sort of. Hope this is useful to someone. * fixes suggested by bgruening for the PR - all adjustments will now apply to all future generated tools :) * add yara mapper ToolFactory - NOT from nf-core. Allows single ended fastq or fasta to be mapped, or a pair of forward and reverse - both must be fastq * small test files still work :) * single quotes for $runme - disappeared mysteriously :( * adding panaroo * Finally fixed the '$runme' suggestion and got the sanitisers not to. * fix profile="22.05" - need to update galaxyxml to fix this and the stdio replacement... * cleanup master branch of fork * update help some prompts add bgperpx - todo add as a parameter * 2.12.2 update Add wiggle track colour and other controls Add bpPerPx in advanced section to control view scale at default open Clarify dependence on remote URI tabix data if uri source used. * bump to 2.12.3 jb2 still passes tests - no breakage yet. * fix JB2VER although not currently used... * Have the no-build plugin for bed colour above and below zero binary working! Involved a substantial simplification of the default_session setup - just needed "configuration": displayId in the display. Simples. * remove copy for strings. * Update tools/jbrowse2/jbrowse2.xml Co-authored-by: Björn Grüning * Update tools/jbrowse2/jbrowse2.xml Co-authored-by: Björn Grüning * fix flake errors and some suggestions * thought I'd got this one... * add the new plugin js * change bed default to not use plugin * add help explaining relationship to the Bigwig extremes to bed features tool and to the advanced control form. * update to 2.13.0 release fix biotools jbrowse entry informative error message if collection has no fasta reference * decrement version suffix back to zero * remove flakery spaces * make genome from history and built in genome non-optional to fix a sentry issue reported and PR suggested by Marius * update to 2.13.1 opportunistically :) * Add collection_type to input collection. It should always be a list Suggestion from Marius - thanks! * change bigwigs to default to global +/- 3sd scaling. makes them much more useful for most purposes - can swap back otherwise local differences can appear to be more important than they really are... use element_identifier for labels instead of name * Bump version :( * update to 2.14.0 remove now missing specific wolf file from 3 old tests. * version bump 2.15.1 fix tool test output counts to match new code * Update to 2.15.4 - a patch to fix a regression in 2.15.3 breaking hic tracks https://github.com/GMOD/jbrowse-components/issues/4583 Have updated vcf and blastxml test files too FWIW --------- Co-authored-by: Björn Grüning --- tools/jbrowse2/jbrowse2.py | 6 ++---- tools/jbrowse2/jbrowse2.xml | 14 +++----------- tools/jbrowse2/macros.xml | 8 ++++---- 3 files changed, 9 insertions(+), 19 deletions(-) diff --git a/tools/jbrowse2/jbrowse2.py b/tools/jbrowse2/jbrowse2.py index 24188ca42b..b8a0024a4b 100644 --- a/tools/jbrowse2/jbrowse2.py +++ b/tools/jbrowse2/jbrowse2.py @@ -411,7 +411,7 @@ def __init__(self, outdir, jbrowse2path): [] ) # for default session - these are read as first line of the assembly .fai self.giURL = GALAXY_INFRASTRUCTURE_URL - self.outdir = outdir + self.outdir = os.path.abspath(outdir) self.jbrowse2path = jbrowse2path os.makedirs(self.outdir, exist_ok=True) self.genome_names = [] @@ -444,7 +444,7 @@ def subprocess_popen(self, command, cwd=True): log.debug(command) p = subprocess.Popen( command, - cwd=self.get_cwd(cwd), + cwd=self.outdir, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, @@ -1440,8 +1440,6 @@ def add_default_session(self, default_data): ) session_views.append(view_json) session_name = default_data.get("session_name", "New session") - for key, value in mapped_chars.items(): - session_name = session_name.replace(value, key) session_json["name"] = session_name if "views" not in session_json: diff --git a/tools/jbrowse2/jbrowse2.xml b/tools/jbrowse2/jbrowse2.xml index 5b863f1204..027617fda0 100644 --- a/tools/jbrowse2/jbrowse2.xml +++ b/tools/jbrowse2/jbrowse2.xml @@ -639,13 +639,10 @@ export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 && - - - + - @@ -697,13 +694,10 @@ export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 && - - - + - @@ -1119,10 +1113,8 @@ export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 && - - + - diff --git a/tools/jbrowse2/macros.xml b/tools/jbrowse2/macros.xml index a8e4f962a9..6300e4ad5d 100644 --- a/tools/jbrowse2/macros.xml +++ b/tools/jbrowse2/macros.xml @@ -1,5 +1,5 @@ - 2.13.1 + 2.15.4 topic_3307 @@ -15,17 +15,17 @@ jbrowse2 biopython bcbio-gff - samtools + samtools pyyaml tabix findutils - hictk + hictk zip \$GALAXY_JBROWSE_SHARED_DIR - 1 + 0