From be5578e24f854364eeae00fa71a8259e143dffd0 Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inra.fr>
Date: Fri, 29 Jan 2021 14:02:02 +0100
Subject: [PATCH] conda migale
---
RunSnake.sh | 1 +
affiliation.smk | 59 ++++++++++++++++++++++++++-----------------------
global.smk | 3 +++
preprocess.smk | 36 ++++++++++++++++--------------
quality.smk | 8 +++++++
5 files changed, 63 insertions(+), 44 deletions(-)
diff --git a/RunSnake.sh b/RunSnake.sh
index 536c232..77636ab 100755
--- a/RunSnake.sh
+++ b/RunSnake.sh
@@ -11,6 +11,7 @@ snakemake \
--cluster-config cluster.json \
--cluster "qsub -V -cwd -N {rule} -o {cluster.out} -e {cluster.err} -q {cluster.queue} -pe thread {threads} {cluster.cluster}" \
--keep-going \
+--restart-times 5 \
--jobs 80 \
--wait-for-files \
--latency-wait 150 \
diff --git a/affiliation.smk b/affiliation.smk
index 6cfddd6..a74736b 100644
--- a/affiliation.smk
+++ b/affiliation.smk
@@ -1,38 +1,28 @@
-rule blastn:
+rule addAffi:
input:
+ biom = "work/dada/dada.biom",
fasta = "work/dada/seqtab.fasta"
output:
- blast = "work/BLAST/seqtab.fasta.blast"
+ biom = "work/FROGS/affiliation.biom",
+ html = "work/FROGS/affiliation.html",
+ log = "work/FROGS/affiliation.log"
threads:
config["THREADS"]
params:
database = config["DATABASE"]
shell:
- "blastn "
- "-num_threads {threads} "
- "-task megablast "
- "-word_size 38 "
- "-max_target_seqs 500 "
- "-outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen' "
- "-query {input.fasta} "
- "-out {output.blast} "
- "-db {params.database} "
-
-rule addAffi:
- input:
- biom = "work/dada/dada.biom",
- fasta = "work/dada/seqtab.fasta",
- blast = "work/BLAST/seqtab.fasta.blast"
- output:
- biom = "work/FROGS/affiliation.biom"
- params:
- database = config["DATABASE"]
- shell:
- "addAffiliation2biom.py "
+ "conda activate frogs-3.2.0 "
+ "&& "
+ "affiliation_OTU.py "
+ "--input-fasta {input.fasta} "
+ "--input-biom {input.biom} "
+ "--nb-cpu {threads} "
+ "--log-file {output.log} "
+ "--output-biom {output.biom} "
+ "--summary {output.html} "
"--reference {params.database} "
- "--blast-file {input.blast} "
- "--biom-in {input.biom} "
- "--biom-out {output.biom} "
+ "&& "
+ "conda deactivate"
rule stats:
input:
@@ -41,10 +31,12 @@ rule stats:
html_cluster = "work/FROGS/clusters_metrics.html",
html_affiliations = "work/FROGS/affiliations_metrics.html"
shell:
+ "conda activate frogs-3.2.0 "
+ "&& "
"clusters_stat.py "
"--input-biom {input.biom} "
"--output-file {output.html_cluster}"
- " ; "
+ "&& "
"affiliations_stat.py "
"--input-biom {input.biom} "
"--output-file {output.html_affiliations} "
@@ -54,6 +46,8 @@ rule stats:
"--tax-consensus-tag blast_taxonomy "
"--identity-tag perc_identity "
"--coverage-tag perc_query_coverage"
+ "&& "
+ "conda deactivate"
rule tree:
input:
@@ -65,12 +59,16 @@ rule tree:
threads:
config["THREADS"]
shell:
- "/projet/galaxyprod/galaxy/tools/FROGS/app/tree.py "
+ "conda activate frogs-3.2.0 "
+ "&& "
+ "tree.py "
"--nb-cpus {threads} "
"--input-otu {input.fasta} "
"--biomfile {input.biom} "
"--html {output.html} "
"--out-tree {output.nwk}"
+ "&& "
+ "conda deactivate"
rule stdBIOM:
input:
@@ -79,11 +77,16 @@ rule stdBIOM:
biom = "work/FROGS/abundance.biom",
tsv = "work/FROGS/multihits.tsv"
shell:
+ "conda activate frogs-3.2.0 "
+ "&& "
"biom_to_stdBiom.py "
"--input-biom {input.biom} "
"--output-biom {output.biom} "
"--output-metadata {output.tsv}"
+ "&& "
+ "conda deactivate"
+localrules: copy
rule copy:
input:
"work/FROGS/{file}"
diff --git a/global.smk b/global.smk
index 4218d09..c239dc2 100644
--- a/global.smk
+++ b/global.smk
@@ -1,3 +1,6 @@
+shell.executable("/bin/bash")
+shell.prefix("source /usr/local/genome/Anaconda2-5.1.0/etc/profile.d/conda.sh;")
+
configfile: "./config.json"
SAMPLES=config["SAMPLES"]
diff --git a/preprocess.smk b/preprocess.smk
index 047b13b..5d09261 100644
--- a/preprocess.smk
+++ b/preprocess.smk
@@ -1,20 +1,24 @@
rule cutadapt:
- input:
- "DATA/{sample}.fastq.gz"
- output:
- "work/cutadapt/{sample}.fastq.gz"
- params:
- five = lambda wildcards: config["FIVE_PRIMER"][wildcards.sample],
- three = lambda wildcards: config["THREE_PRIMER"][wildcards.sample]
- shell:
- "cutadapt "
- "-g {params.five} "
- "-a {params.three} "
- "--error-rate 0.1 "
- "--discard-untrimmed "
- "--match-read-wildcards "
- "-o {output} "
- "{input} "
+ input:
+ "DATA/{sample}.fastq.gz"
+ output:
+ "work/cutadapt/{sample}.fastq.gz"
+ params:
+ five = lambda wildcards: config["FIVE_PRIMER"][wildcards.sample],
+ three = lambda wildcards: config["THREE_PRIMER"][wildcards.sample]
+ shell:
+ "conda activate cutadapt-2.5 "
+ "&& "
+ "cutadapt "
+ "-g {params.five} "
+ "-a {params.three} "
+ "--error-rate 0.1 "
+ "--discard-untrimmed "
+ "--match-read-wildcards "
+ "-o {output} "
+ "{input} "
+ "&& "
+ "conda deactivate"
rule filter:
input:
diff --git a/quality.smk b/quality.smk
index aca3d4f..346084a 100644
--- a/quality.smk
+++ b/quality.smk
@@ -7,10 +7,14 @@ rule fastqc:
params:
output = "work/fastqc/"
shell:
+ "conda activate fastqc-0.11.8 "
+ "&& "
"fastqc "
"{input} "
"--noextract "
"--outdir {params.output} "
+ "&& "
+ "conda deactivate "
rule multiqc:
input:
@@ -20,7 +24,11 @@ rule multiqc:
params:
output = "report/"
shell:
+ "conda activate multiqc-1.8 "
+ "&& "
"multiqc "
"--no-data-dir "
"--outdir {params.output} "
"{input} "
+ "&& "
+ "conda deactivate "
--
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