Split conda enviroments (#30)

* Divided tools in others_env.yaml to separate enviroments. * Fixed a bug in r-virfinder enviroment creation. * Fixed a bug in vardict-java enviroment creation. * Fixed a bug in vardict rule.
jbudis · Jul 14, 2019 · 152ae62 · 152ae62
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diff --git a/docs/conf.py b/docs/conf.py
@@ -26,7 +26,7 @@
 # The short X.Y version
 version = u''
 # The full version, including alpha/beta/rc tags
-release = u'0.9.0'
+release = u'0.9.1'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/enviroments/bamtools.yaml b/enviroments/bamtools.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- bamtools=2.4.1
diff --git a/enviroments/bandage.yaml b/enviroments/bandage.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- bandage=0.8.1
diff --git a/enviroments/bedtools.yaml b/enviroments/bedtools.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- bedtools=2.26.0
diff --git a/enviroments/bismark.yaml b/enviroments/bismark.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- bismark=0.20.0
diff --git a/enviroments/blast.yaml b/enviroments/blast.yaml
@@ -0,0 +1,4 @@
+channels:
+- conda-forge
+dependencies:
+- blast=2.7.1
diff --git a/enviroments/iqtree_env.yaml → enviroments/bowtie.yaml b/enviroments/iqtree_env.yaml → enviroments/bowtie.yaml
@@ -1,4 +1,4 @@
 channels:
 - bioconda
 dependencies:
-- iqtree=1.6.11
+- bowtie=1.1.2
diff --git a/enviroments/bowtie2.yaml b/enviroments/bowtie2.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- bowtie2=2.3.4.3
diff --git a/enviroments/bowtie2_samtools.yaml b/enviroments/bowtie2_samtools.yaml
@@ -0,0 +1,5 @@
+channels:
+- bioconda
+dependencies:
+- bowtie2=2.3.4.3
+- samtools=1.4.1
diff --git a/enviroments/bwa.yaml b/enviroments/bwa.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- bwa=0.7.12
diff --git a/enviroments/bwa_samtools.yaml b/enviroments/bwa_samtools.yaml
@@ -0,0 +1,5 @@
+channels:
+- bioconda
+dependencies:
+- bwa=0.7.12
+- samtools=1.4.1
diff --git a/enviroments/cdhit.yaml b/enviroments/cdhit.yaml
@@ -0,0 +1,4 @@
+channels:
+- agbiome
+dependencies:
+- cdhit=4.6.1
diff --git a/enviroments/clark.yaml b/enviroments/clark.yaml
@@ -0,0 +1,4 @@
+channels:
+- agbiome
+dependencies:
+- clark=1.2.3
diff --git a/enviroments/edger_env.yaml → enviroments/edger.yaml b/enviroments/edger_env.yaml → enviroments/edger.yaml
diff --git a/enviroments/emirge_env.yaml → enviroments/emirge.yaml b/enviroments/emirge_env.yaml → enviroments/emirge.yaml
diff --git a/enviroments/fast-virome-explorer.yaml b/enviroments/fast-virome-explorer.yaml
@@ -0,0 +1,4 @@
+channels:
+- g2554711
+dependencies:
+- fast-virome-explorer=1.1.0.p2
diff --git a/enviroments/fastqc.yaml b/enviroments/fastqc.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- fastqc=0.11.5
diff --git a/enviroments/fastuniq.yaml b/enviroments/fastuniq.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- fastuniq=1.1
diff --git a/enviroments/freebayes.yaml b/enviroments/freebayes.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- freebayes=1.1.0
diff --git a/enviroments/gatk3_env.yaml → enviroments/gatk3.yaml b/enviroments/gatk3_env.yaml → enviroments/gatk3.yaml
diff --git a/enviroments/gatk4.yaml b/enviroments/gatk4.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- gatk4=4.0.7
diff --git a/enviroments/iqtree.yaml b/enviroments/iqtree.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- iqtree=1.5.5
diff --git a/enviroments/kallisto.yaml b/enviroments/kallisto.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- kallisto=0.43.1
diff --git a/enviroments/krona.yaml b/enviroments/krona.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- krona=2.7
diff --git a/enviroments/lefse.yaml b/enviroments/lefse.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- lefse=1.0.8
diff --git a/enviroments/mafft_env.yaml → enviroments/mafft.yaml b/enviroments/mafft_env.yaml → enviroments/mafft.yaml
diff --git a/enviroments/matam_env.yaml → enviroments/matam.yaml b/enviroments/matam_env.yaml → enviroments/matam.yaml
diff --git a/enviroments/metaxa_env.yaml → enviroments/metaxa.yaml b/enviroments/metaxa_env.yaml → enviroments/metaxa.yaml
diff --git a/enviroments/others_env.yaml b/enviroments/others_env.yaml
diff --git a/enviroments/pear.yaml b/enviroments/pear.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- pear=0.9.6
diff --git a/enviroments/pear_pigz.yaml b/enviroments/pear_pigz.yaml
@@ -0,0 +1,6 @@
+channels:
+- bioconda
+- g2554711
+dependencies:
+- pear=0.9.6
+- pigz=2.3.4-0
diff --git a/enviroments/picard.yaml b/enviroments/picard.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- picard=2.18.14
diff --git a/enviroments/pigz.yaml b/enviroments/pigz.yaml
@@ -0,0 +1,4 @@
+channels:
+- conda-forge
+dependencies:
+- pigz=2.3.4-0
diff --git a/enviroments/prokka.yaml b/enviroments/prokka.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- prokka=1.12.0
diff --git a/enviroments/qualimap.yaml b/enviroments/qualimap.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- qualimap=2.2.2c
diff --git a/enviroments/quast_env.yaml → enviroments/quast.yaml b/enviroments/quast_env.yaml → enviroments/quast.yaml
diff --git a/enviroments/r-virfinder.yaml b/enviroments/r-virfinder.yaml
@@ -0,0 +1,4 @@
+channels:
+- g2554711
+dependencies:
+- r-virfinder=1.1
diff --git a/enviroments/rdp_classifier.yaml b/enviroments/rdp_classifier.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- rdp_classifier=2.2
diff --git a/enviroments/rdptools_env.yaml → enviroments/rdptools.yaml b/enviroments/rdptools_env.yaml → enviroments/rdptools.yaml
diff --git a/enviroments/salmon.yaml b/enviroments/salmon.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- salmon=0.12.0
diff --git a/enviroments/samtools.yaml b/enviroments/samtools.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- samtools=1.4.1
diff --git a/enviroments/seqtk.yaml b/enviroments/seqtk.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- seqtk=1.3
diff --git a/enviroments/snpsift.yaml b/enviroments/snpsift.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- snpsift=4.3.1t
diff --git a/enviroments/soapdenovo2_env.yaml → enviroments/soapdenovo2.yaml b/enviroments/soapdenovo2_env.yaml → enviroments/soapdenovo2.yaml
diff --git a/enviroments/sortmerna.yaml b/enviroments/sortmerna.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- sortmerna=2.1b
diff --git a/enviroments/spades.yaml b/enviroments/spades.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- spades=3.10.1
diff --git a/enviroments/trimmomatic.yaml b/enviroments/trimmomatic.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- trimmomatic=0.36
diff --git a/enviroments/trinity_env.yaml → enviroments/trinity.yaml b/enviroments/trinity_env.yaml → enviroments/trinity.yaml
diff --git a/enviroments/unicycler_env.yaml → enviroments/unicycler.yaml b/enviroments/unicycler_env.yaml → enviroments/unicycler.yaml
diff --git a/enviroments/vardict-java.yaml b/enviroments/vardict-java.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- vardict-java=1.5.1
diff --git a/enviroments/vardict.yaml b/enviroments/vardict.yaml
@@ -0,0 +1,6 @@
+channels:
+- bioconda
+- r
+dependencies:
+- vardict=2017.04.18
+- r=3.6.0
diff --git a/enviroments/varscan.yaml b/enviroments/varscan.yaml
@@ -0,0 +1,4 @@
+channels:
+- bioconda
+dependencies:
+- varscan=2.4.3
diff --git a/rules/assembly/assembler/spades.snake b/rules/assembly/assembler/spades.snake
@@ -34,7 +34,7 @@ rule spades__assemble_reads_into_contigs:
         out = 'assembly/{sample}/log/spades.log',
         err = 'assembly/{sample}/log/spades.err'
     conda:
-        config['snakelines_dir'] + '/enviroments/others_env.yaml'
+        config['snakelines_dir'] + '/enviroments/spades.yaml'
     shell:
         """
         spades.py \

diff --git a/rules/assembly/assembler/unicycler.snake b/rules/assembly/assembler/unicycler.snake
@@ -26,7 +26,7 @@ rule unicycler__assemble_reads_into_contigs:
         out = 'assembly/{sample}/log/unicycler.log',
         err = 'assembly/{sample}/log/unicycler.err'
     conda:
-        config['snakelines_dir'] + '/enviroments/unicycler_env.yaml'
+        config['snakelines_dir'] + '/enviroments/unicycler.yaml'
     shell:
         """
         unicycler \

diff --git a/rules/assembly/report/assembly_graph/bandage.snake b/rules/assembly/report/assembly_graph/bandage.snake
@@ -9,7 +9,7 @@ rule bandage__visualise_contig_overlaps:
     output:
         svg = '{path}/{sample}.svg'
     conda:
-        config['snakelines_dir'] + '/enviroments/others_env.yaml'
+        config['snakelines_dir'] + '/enviroments/bandage.yaml'
     shell:
         """
         Bandage image \

diff --git a/rules/assembly/report/quality_report/quast.snake b/rules/assembly/report/quality_report/quast.snake
@@ -22,7 +22,7 @@ rule quast__quality_report_for_assembled_contigs:
     threads:
         int(config['threads'])
     conda:
-        config['snakelines_dir'] + '/enviroments/quast_env.yaml'
+        config['snakelines_dir'] + '/enviroments/quast.yaml'
     shell:
         """
         quast \

diff --git a/rules/classification/contig_based/blast.snake b/rules/classification/contig_based/blast.snake
@@ -62,7 +62,7 @@ rule blast__find_homologues:
     threads:
         int(config['threads'])
     conda:
-        config['snakelines_dir'] + '/enviroments/others_env.yaml'
+        config['snakelines_dir'] + '/enviroments/blast.yaml'
     shell:
         """
         set +e pipefail
@@ -151,7 +151,7 @@ rule blast__prepare_reference_index_for_nucleotide:
     params:
         index_prefix = 'reference/{reference}/blast_index/{reference}'
     conda:
-        config['snakelines_dir'] + '/enviroments/others_env.yaml'
+        config['snakelines_dir'] + '/enviroments/blast.yaml'
     shell:
         """
         makeblastdb \
@@ -185,7 +185,7 @@ rule blast__prepare_reference_index_for_protein:
     params:
         index_prefix = 'reference/{reference}/blast_index/{reference}'
     conda:
-        config['snakelines_dir'] + '/enviroments/others_env.yaml'
+        config['snakelines_dir'] + '/enviroments/blast.yaml'
     shell:
         """
         makeblastdb \

diff --git a/rules/classification/differential_analysis/edger.snake b/rules/classification/differential_analysis/edger.snake
@@ -21,7 +21,7 @@ rule edger__identify_transcripts_with_changed_expression:
         group_by = method_config['group_by'],
         batch = method_config.get('batch', '')
     conda:
-        config['snakelines_dir'] + '/enviroments/edger_env.yaml'
+        config['snakelines_dir'] + '/enviroments/edger.yaml'
     shell:
         '''
         Rscript {input.edger} \

diff --git a/rules/classification/read_based/fast_virome_explorer.snake b/rules/classification/read_based/fast_virome_explorer.snake
@@ -55,7 +55,7 @@ rule fast_virome_explorer__estimate_virome_composition:
         co = '{}'.format(genome_coverage),
         cn = '{}'.format(mapped_reads)
     conda:
-        config['snakelines_dir'] + '/enviroments/others_env.yaml'
+        config['snakelines_dir'] + '/enviroments/fast-virome-explorer.yaml'
     shell:
         '''
         fast_virome_explorer \

diff --git a/rules/classification/read_based/metaxa2.snake b/rules/classification/read_based/metaxa2.snake
@@ -36,7 +36,7 @@ rule metaxa2__classify_reads:
     threads:
         int(config['threads'])
     conda:
-        config['snakelines_dir'] + '/enviroments/metaxa_env.yaml'
+        config['snakelines_dir'] + '/enviroments/metaxa.yaml'
     shell:
         """
         metaxa2 \
@@ -81,7 +81,7 @@ rule metaxa2__create_reference_index:
         out       = 'reference/{reference}/metaxa2_index/log/db.log',
         err       = 'reference/{reference}/metaxa2_index/log/db.err'
     conda:
-        config['snakelines_dir'] + '/enviroments/metaxa_env.yaml'
+        config['snakelines_dir'] + '/enviroments/metaxa.yaml'
     shell:
         """
         metaxa2_dbb \
@@ -120,7 +120,7 @@ rule metaxa2__summarize_classification:
         out                  = 'classification/{reference}/samples/{sample}/log/metaxa2_ttt.log',
         err                  = 'classification/{reference}/samples/{sample}/log/metaxa2_ttt.err'
     conda:
-        config['snakelines_dir'] + '/enviroments/metaxa_env.yaml'
+        config['snakelines_dir'] + '/enviroments/metaxa.yaml'
     shell:
         """
         TAXONOMY={input.taxonomy}

diff --git a/rules/classification/read_based/rdp.snake b/rules/classification/read_based/rdp.snake
@@ -22,7 +22,7 @@ rule rdp__classify_reads:
     params:
         confidence = method_config.get('confidence', RDP_DEFAULT_CONFIDENCE)
     conda:
-        config['snakelines_dir'] + '/enviroments/rdptools_env.yaml'
+        config['snakelines_dir'] + '/enviroments/rdptools.yaml'
     shell:
         '''
         rdp_classifier classify \

diff --git a/rules/classification/report/summary/fasta_summary.snake b/rules/classification/report/summary/fasta_summary.snake
@@ -123,7 +123,7 @@ rule fasta_summary__mapped_reads:
     output:
         tsv = '{indir}/annotation/{name}/attributes/mapped_reads.tsv'
     conda:
-        config['snakelines_dir'] + '/enviroments/others_env.yaml'
+        config['snakelines_dir'] + '/enviroments/samtools.yaml'
     shell:
         """
         echo -e '\tMapped reads' > {output.tsv}