osx

maxplanck-ie · Jun 5, 2024 · 40b5010 · 40b5010
1 parent 4feee8a
commit 40b5010
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Showing 8 changed files with 18 additions and 10 deletions.
diff --git a/.github/workflows/osx.yml b/.github/workflows/osx.yml
@@ -52,5 +52,6 @@ jobs:
       - name: createEnvsOSX
         run: |
           micromamba activate snakePipes_CI
+          conda config --add subdirs osx-64
           snakePipes createEnvs --autodetectCondaEnvDir --only ${{matrix.envs}}
      
diff --git a/snakePipes/common_functions.py b/snakePipes/common_functions.py
@@ -23,6 +23,7 @@ def set_env_yamls():
     return {'CONDA_SHARED_ENV': 'envs/shared.yaml',
             'CONDA_CREATE_INDEX_ENV': 'envs/createIndices.yaml',
             'CONDA_RNASEQ_ENV': 'envs/rna_seq.yaml',
+            'CONDA_SALMON_ENV': 'envs/salmon.yaml',
             'CONDA_SLEUTH_ENV': 'envs/sleuth.yaml',
             'CONDA_RMATS_ENV': 'envs/rMats.yaml',
             'CONDA_scRNASEQ_ENV': 'envs/sc_rna_seq.yaml',

diff --git a/snakePipes/shared/rules/Salmon.snakefile b/snakePipes/shared/rules/Salmon.snakefile
@@ -80,7 +80,7 @@ else:
             gtf = genes_gtf,
             lib_type = getSalmon_libtype(pairedEnd, libraryType)
         threads: 8
-        conda: CONDA_RNASEQ_ENV
+        conda: CONDA_SALMON_ENV
         shell: """
             salmon quant -p {threads} --softclipOverhangs --validateMappings --numBootstraps 50 -i {params.index} -l {params.lib_type} -r {input.fastq} -o {params.outdir} 2> {log}
             """

diff --git a/snakePipes/shared/rules/Salmon_allelic.snakefile b/snakePipes/shared/rules/Salmon_allelic.snakefile
@@ -79,7 +79,7 @@ samtools fastq -1 {output.r1} -2 {output.r2} -0 /dev/null -s /dev/null -n  \\
             gtf = genes_gtf,
             lib_type = getSalmon_libtype(pairedEnd, libraryType)
         threads: 8
-        conda: CONDA_RNASEQ_ENV
+        conda: CONDA_SALMON_ENV
         shell: """
             salmon quant -p {threads} --softclipOverhangs --validateMappings --numBootstraps 50 -i {params.index} -l {params.lib_type} -1 {input.r1} -2 {input.r2} -o {params.outdir} 2> {log}
             """
@@ -114,7 +114,7 @@ samtools fastq -1 /dev/null -2 /dev/null -0 /dev/null -s {output.r1} -n  \\
             gtf = genes_gtf,
             lib_type = getSalmon_libtype(pairedEnd, libraryType)
         threads: 8
-        conda: CONDA_RNASEQ_ENV
+        conda: CONDA_SALMON_ENV
         shell: """
             salmon quant -p {threads} --softclipOverhangs --validateMappings --numBootstraps 50 -i {params.index} -l {params.lib_type} -r {input.fastq} -o {params.outdir} 2> {log}
             """

diff --git a/snakePipes/shared/rules/createIndices.snakefile b/snakePipes/shared/rules/createIndices.snakefile
@@ -411,7 +411,7 @@ rule Salmon_index_joint_fa:
         err = "SalmonIndex_RNAVelocity/logs/SalmonIndex.err",
         out = "SalmonIndex_RNAVelocity/logs/SalmonIndex.out"
     threads: lambda wildcards: 16 if 16<max_thread else max_thread
-    conda: CONDA_RNASEQ_ENV
+    conda: CONDA_SALMON_ENV
     shell:"""
         cat {input.joint_fasta} {input.genome_fasta} > {output.seq_fa}
         salmon index -p {threads} -t {output.seq_fa} -d {input.decoys} -i SalmonIndex_RNAVelocity {params.salmonIndexOptions} > {log.out} 2> {log.err}

diff --git a/snakePipes/shared/rules/envs/rna_seq.yaml b/snakePipes/shared/rules/envs/rna_seq.yaml
@@ -1,4 +1,4 @@
-name: snakepipes_RNAseq_environment_2.0
+name: snakepipes_RNAseq_environment_3.0
 channels:
  - conda-forge
  - bioconda
@@ -9,8 +9,8 @@ dependencies:
  - subread = 2.0.1
  - hisat2 = 2.2.1
  - star = 2.7.10b
- - salmon = 1.10.1
- - r-base = 4.1.3
+# - salmon = 1.10.1
+ - r-base = 4.3.0
  - r-wasabi
  - r-dplyr
  - r-ggplot2
@@ -20,7 +20,7 @@ dependencies:
  - pandoc
  - r-dt
  - r-rcolorbrewer
- - bioconductor-deseq2
+ - bioconductor-deseq2 = 1.42.0
  - bioconductor-tximport
  - r-knitcitations
  - bioconductor-apeglm

diff --git a/snakePipes/shared/rules/envs/salmon.yaml b/snakePipes/shared/rules/envs/salmon.yaml
@@ -0,0 +1,6 @@
+name: snakepipes_salmon_environment_1.0
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - salmon = 1.10.1
diff --git a/snakePipes/shared/rules/scRNAseq_Alevin.snakefile b/snakePipes/shared/rules/scRNAseq_Alevin.snakefile
@@ -39,7 +39,7 @@ rule SalmonAlevin:
             out =  "Alevin/logs/alevin.{sample}.out",
             err = "Alevin/logs/alevin.{sample}.err"
         #Use RNAseq env because Salmon already installed there (no need for duplication).
-        conda: CONDA_RNASEQ_ENV
+        conda: CONDA_SALMON_ENV
         threads: 8
         shell:"""
             salmon alevin -l {params.libtype} -1 {input.R1} -2 {input.R2} {params.protocol} -i {params.index} -p {threads} -o {params.outdir} --tgMap {input.tgMap} --dumpFeatures --dumpMtx --numCellBootstraps 100 > {log.out} 2> {log.err}
@@ -124,7 +124,7 @@ rule AlevinForVelocity:
             out =  "AlevinForVelocity/logs/alevin.{sample}.out",
             err = "AlevinForVelocity/logs/alevin.{sample}.err"
         #Use RNAseq env because Salmon already installed there (no need for duplication).
-        conda: CONDA_RNASEQ_ENV
+        conda: CONDA_SALMON_ENV
         threads: 8
         shell:"""
             salmon alevin -l {params.libtype} -1 {input.R1} -2 {input.R2} {params.protocol} -i {params.velo_index} -p {threads} -o {params.outdir} --tgMap {params.tgMap} --dumpFeatures --dumpMtx --numCellBootstraps 100 > {log.out} 2> {log.err}