Just Bio (#36)

* build samtools * bio hash not ready * Remove unnecessary bio scripts and input setup script * Refactor bio scripts and input setup - Renamed `bio/inputs.sh` to `bio/deps.sh` and removed unnecessary code. - Updated `bio/run.sh` to use the correct input file name. - Removed unused code from `bio/input.sh`. - Cleaned up `bio/verify.sh` and added comments. Closes #27 * nlp no pass? * nlp? * Rename input_all to input and add input_small Signed-off-by: Evangelos Lamprou <[email protected]> * Fix verify output format Signed-off-by: Evangelos Lamprou <[email protected]> * Fix bio Signed-off-by: Evangelos Lamprou <[email protected]> --------- Signed-off-by: Evangelos Lamprou <[email protected]> Co-authored-by: Zhuoxuan Zhang <[email protected]> Co-authored-by: Evangelos Lamprou <[email protected]>
binpash · Jan 3, 2025 · 62f85ab · 62f85ab
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commit 62f85ab
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        benchmark: [nlp, file-enc, unix50, log-analysis, max-temp, media-conv, sklearn, covid-mts, riker, oneliners, web-index]
+        benchmark: [nlp, file-enc, unix50, log-analysis, max-temp, media-conv, sklearn, covid-mts, riker, oneliners, web-index, bio]
 
     steps:
       - name: Checkout code

diff --git a/bio/.gitignore b/bio/.gitignore
@@ -0,0 +1,2 @@
+inputs
+outputs
diff --git a/bio/bio-align/bio.sh b/bio/bio-align/bio.sh
diff --git a/bio/bio-align/genome-diff.sh b/bio/bio-align/genome-diff.sh
diff --git a/bio/bio-align/genquality.sh b/bio/bio-align/genquality.sh
diff --git a/bio/bio1/README b/bio/bio1/README
diff --git a/bio/bio1/bam_to_sam.sh b/bio/bio1/bam_to_sam.sh
diff --git a/bio/bio1/bio2.sh b/bio/bio1/bio2.sh
diff --git a/bio/bio1/bio3.sh b/bio/bio1/bio3.sh
diff --git a/bio/bio1/convert_to_fast.sh b/bio/bio1/convert_to_fast.sh
diff --git a/bio/bio1/generate_single_chrom.sh b/bio/bio1/generate_single_chrom.sh
diff --git a/bio/bio1/remove_adapter.sh b/bio/bio1/remove_adapter.sh
diff --git a/bio/bio1/setup.sh b/bio/bio1/setup.sh
diff --git a/bio/bio1/trim_primers.sh b/bio/bio1/trim_primers.sh
diff --git a/bio/cleanup.sh b/bio/cleanup.sh
@@ -0,0 +1 @@
+rm -rf input output