Commit f687d721 authored by mmassaviol's avatar mmassaviol
Browse files

Debug mitoz_annotate (multiples fastqs)

Debug circos (increase max_points_per_track)
parent 2d2f6153
......@@ -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 \
......
......@@ -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
......
......@@ -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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