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fix!: pin dependency version in all wrapper conda env yamls (#492)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bedtools | ||
| - alfred >=0.2.8,<0.3.0 | ||
| - jq | ||
| - bedtools==2.31.1 | ||
| - alfred==0.2.8 | ||
| - jq==1.7.1 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,5 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - arcas-hla | ||
| - arcas-hla==0.6.0 |
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10 changes: 5 additions & 5 deletions
10
snappy_wrappers/wrappers/baf_file_generation/environment.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bcftools ==1.15.1 | ||
| - htslib ==1.15.1 | ||
| - ucsc-wigtobigwig | ||
| - bcftools==1.15.1 | ||
| - htslib==1.15.1 | ||
| - ucsc-wigtobigwig==447 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -2,5 +2,5 @@ channels: | |
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bbmap =39 | ||
| - openjdk >= 8 | ||
| - bbmap==39.06 | ||
| - openjdk==20.0.2 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bcftools ==1.15 | ||
| - htslib ==1.15 | ||
| - bcftools==1.15 | ||
| - htslib==1.15 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,6 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - r | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bcftools ==1.3.1 | ||
| - htslib ==1.3.2 | ||
| - bcftools==1.3.1 | ||
| - htslib==1.3.2 |
7 changes: 3 additions & 4 deletions
7
snappy_wrappers/wrappers/bed_jaccard_operations/environment.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,5 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - r | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bedtools ==2.26.0 | ||
| - bedtools==2.26.0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,5 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - r | ||
| dependencies: | ||
| - bedtools ==2.26.0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,5 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - r | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - htslib ==1.4.1 | ||
| - htslib==1.4.1 |
17 changes: 8 additions & 9 deletions
17
snappy_wrappers/wrappers/cbioportal/generate_cna/environment.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,14 +1,13 @@ | ||
| name: generate_cna | ||
|
|
||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - r | ||
| - conda-forge | ||
| - bioconda | ||
|
|
||
| dependencies: | ||
| - r-base | ||
| - r-tidyverse | ||
| - r-igraph | ||
| - bioconductor-genomicranges | ||
| - bioconductor-genomicfeatures | ||
| - bioconductor-deseq2 | ||
| - r-base==4.3.3 | ||
| - r-tidyverse==2.0.0 | ||
| - r-igraph==2.0.2 | ||
| - bioconductor-genomicranges==1.54.1 | ||
| - bioconductor-genomicfeatures==1.54.1 | ||
| - bioconductor-deseq2==1.42.0 |
17 changes: 8 additions & 9 deletions
17
snappy_wrappers/wrappers/cbioportal/merge_tables/environment.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,14 +1,13 @@ | ||
| name: merge_tables | ||
|
|
||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - r | ||
| - conda-forge | ||
| - bioconda | ||
|
|
||
| dependencies: | ||
| - r-base | ||
| - r-tidyverse | ||
| - r-igraph | ||
| - bioconductor-genomicranges | ||
| - bioconductor-genomicfeatures | ||
| - bioconductor-deseq2 | ||
| - r-base==4.3.3 | ||
| - r-tidyverse==2.0.0 | ||
| - r-igraph==2.0.2 | ||
| - bioconductor-genomicranges==1.54.1 | ||
| - bioconductor-genomicfeatures==1.54.1 | ||
| - bioconductor-deseq2==1.42.0 |
11 changes: 5 additions & 6 deletions
11
snappy_wrappers/wrappers/cnvetti/on_target/coverage/environment.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,7 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - r | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - cnvetti ==0.2.0 | ||
| - bcftools ==1.9 | ||
| - htslib ==1.9 | ||
| - cnvetti==0.2.0 | ||
| - bcftools==1.9 | ||
| - htslib==1.9 |
35 changes: 17 additions & 18 deletions
35
snappy_wrappers/wrappers/cnvetti/on_target/postprocess/environment.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,20 +1,19 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - anaconda | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - r | ||
| - r-rcpp | ||
| - r-dplyr | ||
| - r-assertthat | ||
| - r-matrixstats | ||
| - bioconductor-copywriter | ||
| - bioconductor-dnacopy | ||
| - bioconductor-cghcall | ||
| - bioconductor-rsamtools | ||
| - bioconductor-org.hs.eg.db | ||
| - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene | ||
| - bcftools ==1.5 | ||
| - samtools ==1.5 | ||
| - htslib ==1.5 | ||
| - openblas | ||
| - r-base==4.2 | ||
| - r-rcpp==1.0.12 | ||
| - r-dplyr==1.1.4 | ||
| - r-assertthat==0.2.1 | ||
| - r-matrixstats==1.2.0 | ||
| - bioconductor-copywriter==2.29.0 | ||
| - bioconductor-dnacopy==1.72.0 | ||
| - bioconductor-cghcall==2.60.0 | ||
| - bioconductor-rsamtools==2.14.0 | ||
| - bioconductor-org.hs.eg.db==3.16.0 | ||
| - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene==3.2.2 | ||
| - bcftools==1.5 | ||
| - samtools==1.5 | ||
| - htslib==1.5 | ||
| - openblas==0.3.26 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,7 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - r | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - cnvetti ==0.2.0 | ||
| - bcftools ==1.9 | ||
| - htslib ==1.9 | ||
| - cnvetti==0.2.0 | ||
| - bcftools==1.9 | ||
| - htslib==1.9 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,7 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - r | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - python >3.7 | ||
| - cnvkit | ||
| - htslib | ||
| - python==3.10.14 | ||
| - cnvkit==0.9.10 | ||
| - htslib==1.19.1 |
11 changes: 5 additions & 6 deletions
11
snappy_wrappers/wrappers/cnvkit/postprocess/environment.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,7 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - r | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - r-base | ||
| - bioconductor-genomicranges | ||
| - htslib | ||
| - r-base==4.3.3 | ||
| - bioconductor-genomicranges==1.54.1 | ||
| - htslib==1.19 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,7 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - base | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - control-freec | ||
| - sambamba | ||
| - bcftools | ||
| - control-freec==11.6 | ||
| - sambamba==1.0 | ||
| - bcftools==1.19 |
26 changes: 12 additions & 14 deletions
26
snappy_wrappers/wrappers/control_freec/transform/environment.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,16 +1,14 @@ | ||
| channels: | ||
| - bioconda | ||
| - conda-forge | ||
| - anaconda | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - r-base | ||
| - r-tidyverse | ||
| - bioconductor-annotationdbi | ||
| - bioconductor-bsgenome | ||
| - bioconductor-genomicranges | ||
| - bioconductor-org.hs.eg.db | ||
| - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene | ||
| - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene | ||
| - bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 | ||
| - bioconductor-bsgenome.hsapiens.ucsc.hg38 | ||
|
|
||
| - r-base==4.3.3 | ||
| - r-tidyverse==2.0.0 | ||
| - bioconductor-annotationdbi==1.64.1 | ||
| - bioconductor-bsgenome==1.70.1 | ||
| - bioconductor-genomicranges==1.54.1 | ||
| - bioconductor-org.hs.eg.db==3.18.0 | ||
| - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene==3.2.2 | ||
| - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene==3.18.0 | ||
| - bioconductor-bsgenome.hsapiens.1000genomes.hs37d5==0.99.1 | ||
| - bioconductor-bsgenome.hsapiens.ucsc.hg38==1.4.5 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,23 +1,22 @@ | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - anaconda | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - r=3.6 | ||
| - r-rcpp | ||
| - r-dplyr | ||
| - r-assertthat | ||
| - r-matrixstats | ||
| - bioconductor-copywriter | ||
| - bioconductor-dnacopy | ||
| - bioconductor-cghcall | ||
| - bioconductor-rsamtools | ||
| - bioconductor-org.hs.eg.db | ||
| - bioconductor-ensdb.hsapiens.v75 | ||
| - bioconductor-ensdb.hsapiens.v86 | ||
| - bioconductor-txdb.hsapiens.ucsc.hg19.knownGene | ||
| - bioconductor-txdb.hsapiens.ucsc.hg38.knownGene | ||
| - bcftools | ||
| - samtools | ||
| - htslib | ||
| - openblas | ||
| - r-base==3.6 | ||
| - r-rcpp==1.0.6 | ||
| - r-dplyr==1.0.6 | ||
| - r-assertthat==0.2.1 | ||
| - r-matrixstats==0.58.0 | ||
| - bioconductor-copywriter==2.18.0 | ||
| - bioconductor-dnacopy==1.60.0 | ||
| - bioconductor-cghcall==2.48.0 | ||
| - bioconductor-rsamtools==2.2.0 | ||
| - bioconductor-org.hs.eg.db==3.10.0 | ||
| - bioconductor-ensdb.hsapiens.v75==2.99.0 | ||
| - bioconductor-ensdb.hsapiens.v86==2.99.0 | ||
| - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene==3.2.2 | ||
| - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene==3.10.0 | ||
| - bcftools==1.12 | ||
| - samtools==1.12 | ||
| - htslib==1.12 | ||
| - openblas==0.3.12 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,6 @@ | ||
| channels: | ||
| - r | ||
| - conda-forge | ||
| - bioconda | ||
| - https://conda.anaconda.org/dranew | ||
| - conda-forge | ||
| dependencies: | ||
| - defuse ==0.8.1 |
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