Commit 5192ea01 authored by khalid's avatar khalid
Browse files
parents d9885ab2 f687d721
......@@ -19,16 +19,18 @@ RUN cd /opt/biotools \
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV LC_ALL en_US.UTF-8
RUN mkdir -p /share/apps/bin \
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE 3838
......
......@@ -13,16 +13,18 @@ RUN apt install -y gnuplot
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV LC_ALL en_US.UTF-8
RUN mkdir -p /share/apps/bin \
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE 3838
......
......@@ -59,16 +59,18 @@ RUN cd /opt/biotools \
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV LC_ALL en_US.UTF-8
RUN mkdir -p /share/apps/bin \
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE 3838
......
......@@ -28,16 +28,18 @@ RUN cd /opt/biotools \
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV LC_ALL en_US.UTF-8
RUN mkdir -p /share/apps/bin \
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE 3838
......
......@@ -61,16 +61,18 @@ RUN cd /opt/biotools \
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV LC_ALL en_US.UTF-8
RUN mkdir -p /share/apps/bin \
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE 3838
......
......@@ -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 \
......@@ -71,16 +72,18 @@ RUN cd /opt/biotools \
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV LC_ALL en_US.UTF-8
RUN mkdir -p /share/apps/bin \
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE 3838
......
......@@ -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
......
......@@ -21,16 +21,18 @@ RUN Rscript -e 'BiocManager::install("SNPRelate", version = "3.8",Ncpus=8, clean
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV LC_ALL en_US.UTF-8
RUN mkdir -p /share/apps/bin \
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE 3838
......
......@@ -44,16 +44,18 @@ RUN Rscript -e 'BiocManager::install("SNPRelate", version = "3.8",Ncpus=8, clean
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV LC_ALL en_US.UTF-8
RUN mkdir -p /share/apps/bin \
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE 3838
......
......@@ -44,16 +44,18 @@ RUN Rscript -e 'BiocManager::install("BiocParallel", version = "3.8",Ncpus=8, cl
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV LC_ALL en_US.UTF-8
RUN mkdir -p /share/apps/bin \
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE 3838
......
......@@ -60,16 +60,18 @@ RUN apt install -y tabix
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV LC_ALL en_US.UTF-8
RUN mkdir -p /share/apps/bin \
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE 3838
......
......@@ -45,16 +45,18 @@ RUN cd /opt/biotools \
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV LC_ALL en_US.UTF-8
RUN mkdir -p /share/apps/bin \
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE 3838
......
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