| Previous changeset 44:e7cac7790476 (2018-04-25) Next changeset 46:d273453b30bb (2019-05-07) |
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Commit message:
planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty |
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modified:
1_map_reads.xml 2_call_sites.xml 3_filter_regions.xml 4_merge_sites.xml 5_call_consensus.xml 6_merge_vcfs.xml 7_smp_matrix.xml |
| 1_map_reads.xml |
| diff -r e7cac7790476 -r f58616a4b2f3 1_map_reads.xml |
| 1_map_reads.xml |
| --- a/1_map_reads.xml Wed Apr 25 16:35:27 2018 -0400 +++ b/1_map_reads.xml Tue May 07 11:44:12 2019 -0400 @@ -4,7 +4,7 @@ <requirement type="package" version="1.0.6">bzip2</requirement> <requirement type="package" version="2.3.4">bowtie2</requirement> <requirement type="package" version="1.5.11">boto3</requirement> - <!-- <requirement type="package" version="3.5">python</requirement> --> + <requirement type="package" version="3.6">python</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && |
| 2_call_sites.xml |
| diff -r e7cac7790476 -r f58616a4b2f3 2_call_sites.xml |
| 2_call_sites.xml |
| --- a/2_call_sites.xml Wed Apr 25 16:35:27 2018 -0400 +++ b/2_call_sites.xml Tue May 07 11:44:12 2019 -0400 @@ -7,11 +7,11 @@ <requirement type="package">picard</requirement> <requirement type="package">varscan</requirement> <requirement type="package" version="1.5.11">boto3</requirement> - <!-- <requirement type="package" version="3.5">python</requirement> --> + <requirement type="package" version="3.6">python</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && - env && + # env && python $__tool_directory__/snp-cache.py snp_sitecalls "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)" -c " |
| 3_filter_regions.xml |
| diff -r e7cac7790476 -r f58616a4b2f3 3_filter_regions.xml |
| 3_filter_regions.xml |
| --- a/3_filter_regions.xml Wed Apr 25 16:35:27 2018 -0400 +++ b/3_filter_regions.xml Tue May 07 11:44:12 2019 -0400 @@ -5,11 +5,11 @@ <requirement type="package" version="1.0.6">bzip2</requirement> <requirement type="package" version="1.0.1">snp-pipeline</requirement> <requirement type="package" version="1.5.11">boto3</requirement> - <!-- <requirement type="package" version="3.5">python</requirement> --> + <requirement type="package" version="3.6">python</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && - env && + # env && mkdir -p ./samples/sample/ && cp $calls ./samples/sample/var.flt.vcf && echo "\$PWD/samples/sample" > ./alignment.txt && |
| 4_merge_sites.xml |
| diff -r e7cac7790476 -r f58616a4b2f3 4_merge_sites.xml |
| 4_merge_sites.xml |
| --- a/4_merge_sites.xml Wed Apr 25 16:35:27 2018 -0400 +++ b/4_merge_sites.xml Tue May 07 11:44:12 2019 -0400 @@ -5,11 +5,11 @@ <requirement type="package" version="1.2">samtools</requirement> <requirement type="package" version="1.0.6">bzip2</requirement> <requirement type="package" version="1.0.1">snp-pipeline</requirement> - <!-- <requirement type="package" version="3.5">python</requirement> --> + <requirement type="package" version="3.6">python</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && - env && + # env && python $__tool_directory__/snp-wind.py ./ #for $call in $calls -n $call.element_identifier -f $call |
| 5_call_consensus.xml |
| diff -r e7cac7790476 -r f58616a4b2f3 5_call_consensus.xml |
| 5_call_consensus.xml |
| --- a/5_call_consensus.xml Wed Apr 25 16:35:27 2018 -0400 +++ b/5_call_consensus.xml Tue May 07 11:44:12 2019 -0400 @@ -4,11 +4,11 @@ <requirement type="package" version="1.0.6">bzip2</requirement> <requirement type="package" version="1.0.1">snp-pipeline</requirement> <requirement type="package" version="1.5.11">boto3</requirement> - <!-- <requirement type="package" version="3.5">python</requirement> --> + <requirement type="package" version="3.6">python</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && - env && + # env && #set $identifier = $call_pileup.name.split(' ')[0] python $__tool_directory__/snp-cache.py snp_consenus_calls "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)" |
| 6_merge_vcfs.xml |
| diff -r e7cac7790476 -r f58616a4b2f3 6_merge_vcfs.xml |
| 6_merge_vcfs.xml |
| --- a/6_merge_vcfs.xml Wed Apr 25 16:35:27 2018 -0400 +++ b/6_merge_vcfs.xml Tue May 07 11:44:12 2019 -0400 @@ -5,12 +5,12 @@ <requirement type="package" version="1.0.6">bzip2</requirement> <requirement type="package" version="1.0.1">snp-pipeline</requirement> <requirement type="package" version="0.2.5">tabix</requirement> - <!-- <requirement type="package" version="3.5">python</requirement> --> + <requirement type="package" version="3.6">python</requirement> <requirement type="package" version="1.6">htslib</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && - env && + # env && ls -lah \$CONDA_DEFAULT_ENV/bin && ls -lah \$CONDA_DEFAULT_ENV/lib && python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf" |
| 7_smp_matrix.xml |
| diff -r e7cac7790476 -r f58616a4b2f3 7_smp_matrix.xml |
| 7_smp_matrix.xml |
| --- a/7_smp_matrix.xml Wed Apr 25 16:35:27 2018 -0400 +++ b/7_smp_matrix.xml Tue May 07 11:44:12 2019 -0400 @@ -5,11 +5,11 @@ <requirement type="package" version="1.0.6">bzip2</requirement> <requirement type="package" version="1.0.1">snp-pipeline</requirement> <requirement type="package" version="0.2.5">tabix</requirement> - <!-- <requirement type="package" version="3.5">python</requirement> --> + <requirement type="package" version="3.6">python</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && - env && + # env && python $__tool_directory__/snp-wind.py ./ -p "consensus.fasta" #for $fa in sorted($cons, key=lambda f: f.element_identifier) -n $fa.element_identifier -f $fa |