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mmassaviol
WApps
Commits
f687d721
Commit
f687d721
authored
Dec 11, 2019
by
mmassaviol
Browse files
Debug mitoz_annotate (multiples fastqs)
Debug circos (increase max_points_per_track)
parent
2d2f6153
Changes
3
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Mito_Assembler_Megahit/Dockerfile
View file @
f687d721
...
...
@@ -30,7 +30,8 @@ RUN apt-get install -y circos \
&&
cd
/opt/biotools
&&
wget http://circos.ca/distribution/circos-current.tgz
\
&&
tar
-xzf
circos-current.tgz
\
&&
rm
-rf
circos-current.tgz
\
&&
mv
circos
*
circos_current
&&
mv
circos
*
circos_current
\
&&
sed
-i
's/max_points_per_track.*/max_points_per_track = 40000/'
/opt/biotools/circos_current/etc/housekeeping.conf
RUN
cd
/opt/biotools
\
&&
wget https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2
\
...
...
Mito_Assembler_Megahit/files/Snakefile
View file @
f687d721
...
...
@@ -287,7 +287,7 @@ rule mitoz_annotate_SE:
clade = config["clade"],
sample_suffix = config["sample_suffix"]
shell:
"cat {input.read} > reads_R1.{params.sample_suffix} "
"cat {input.read} >
{params.results_dir}/
reads_R1.{params.sample_suffix} "
"&& /opt/biotools/release_MitoZ_v2.4-alpha/MitoZ.py annotate "
"--fastq1 reads_R1.{params.sample_suffix} "
#"--fq_size 0 "
...
...
@@ -319,7 +319,7 @@ rule mitoz_annotate_SE:
"else \n"
" mv circos.png circos_mqc.png \n"
"fi \n"
"rm reads_R1.{params.sample_suffix} "
"rm
{params.results_dir}/
reads_R1.{params.sample_suffix} "
rule mitoz_annotate_PE:
input:
...
...
@@ -338,8 +338,8 @@ rule mitoz_annotate_PE:
clade = config["clade"],
sample_suffix = config["sample_suffix"]
shell:
"cat {input.read} > reads_R1.{params.sample_suffix} "
"&& cat {input.read2} > reads_R2.{params.sample_suffix} "
"cat {input.read} >
{params.results_dir}/
reads_R1.{params.sample_suffix} "
"&& cat {input.read2} >
{params.results_dir}/
reads_R2.{params.sample_suffix} "
"&& /opt/biotools/release_MitoZ_v2.4-alpha/MitoZ.py annotate "
"--fastq1 reads_R1.{params.sample_suffix} "
"--fastq2 reads_R2.{params.sample_suffix} "
...
...
@@ -372,8 +372,8 @@ rule mitoz_annotate_PE:
"else \n"
" mv circos.png circos_mqc.png \n"
"fi \n"
"rm reads_R1.{params.sample_suffix} "
"&& rm reads_R2.{params.sample_suffix} "
"rm
{params.results_dir}/
reads_R1.{params.sample_suffix} "
"&& rm
{params.results_dir}/
reads_R2.{params.sample_suffix} "
ruleorder: mitoz_annotate_PE > mitoz_annotate_SE
...
...
Mito_Assembler_Megahit/files/singularity.def
View file @
f687d721
...
...
@@ -110,6 +110,7 @@ singularity run --app appName this_container.sif
rm -rf circos-current.tgz
mv circos* circos_current
echo 'export PATH="/opt/biotools/circos_current/bin:$PATH"' >>$SINGULARITY_ENVIRONMENT
sed -i 's/max_points_per_track.*/max_points_per_track = 40000/' /opt/biotools/circos_current/etc/housekeeping.conf
cd /opt/biotools
wget https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2
...
...
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