Commit 46bcfbed authored by Lena Hersemann's avatar Lena Hersemann

Merge branch 'master' of git.mpi-cbg.de:bioinfo/ngs_tools

parents 33b07718 45bf671a
......@@ -33,7 +33,7 @@ if [[ ! -f $picardJar ]]; then
exit 1
fi
export JL_FORCE_LOCAL=true
#export JL_FORCE_LOCAL=true
for bamFile in $bamFiles ; do
# DEBUG bamFile=$(ls $bamFiles | head -n1)
......@@ -51,6 +51,12 @@ jl wait --report .dupanlysis || { echo "duplicate analysis failed" >&2; exit 1;
## todo expose gtf as script parameter
gtfFile=${IGENOME}/Annotation/Genes/genes.gtf
if [[ ! -f $gtfFile ]]; then
echo "gtf file '$gtfFile' do not exist" >&2
exit 1
fi
# R --args $gtfFile ${outputDir}/*.markdup.bam
# ll $gtfFile ${outputDir}/*.markdup.bam
rendr_snippet "duplicate_anlysis" <<"EOF" $gtfFile ${outputDir}/*.markdup.bam
......
#!/usr/bin/env bash
screen -R dupradar
export NGS_TOOLS="/projects/bioinfo/$(whoami)/scripts/ngs_tools"
source ${NGS_TOOLS}/dge_workflow/dge_utils.sh
export PATH=${NGS_TOOLS}/dge_workflow:$PATH
PRJ_DATA=/projects/bioinfo/misc/dup_radar_refs
mcdir ${PRJ_DATA}
## fam72d_transfection_seq
mcdir ${PRJ_DATA}/fam72d_transfection_seq
export IGENOME=/projects/bioinfo/igenomes/Mus_musculus/Ensembl_v81/GRCm38
bamFiles=$(ls /projects/bioinfo/brandl/data/fam72d_transfection_seq/alignments/*bam)
#ll ${IGENOME} $bamFiles
dge_analyze_duplicates.sh ${bamFiles} &
## meyer_rnaseq
mcdir ${PRJ_DATA}/meyer_rnaseq
export IGENOME=/projects/bioinfo/igenomes/Mus_musculus/Ensembl_v81/GRCm38
bamFiles=$(ls /projects/bioinfo/brandl/data/meyer_rnaseq/alignments/*bam)
#ls $bamFiles
dge_analyze_duplicates.sh ${bamFiles} &
## xing_rnaseq
mcdir ${PRJ_DATA}/xing_rnaseq
export IGENOME=/projects/bioinfo/igenomes/Mus_musculus/Ensembl_v81/GRCm38
bamFiles=$(ls /projects/bioinfo/data/xing_11b_rnaseq/alignments/*bam)
#ls $bamFiles
dge_analyze_duplicates.sh -${bamFiles} &
wait
mailme "dupradar refs done"
## integrate stats for report overlay
rendr_snippet "dupstats_integration" <<"EOF"
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.39/R/core_commons.R")
EOF
#bi
cd /net/mack/lustre/projects/bioinfo/scripts/ngs_tools/dev/misc/docker_image/
cd /net/mack/lustre/projects/bioinfo/holger/scripts/ngs_tools//misc/docker_image/
docker build -t bioinfo_base .
docker run -it bioinfo_base
......
......@@ -191,7 +191,7 @@ wget -O picard_tools/picard_v${picardVersion}.jar -N https://github.com/broadins
cd /projects/bioinfo/igenomes
#export NGS_TOOLS=/net/mack/lustre/projects/bioinfo/scripts/ngs_tools/dev
#export NGS_TOOLS=/net/mack/lustre/projects/bioinfo/holger/scripts/ngs_tools/
export NGS_TOOLS=/projects/bioinfo/scripts/ngs_tools/dev
source ${NGS_TOOLS}/dge_workflow/dge_utils.sh
source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.38/bash/core_utils.sh 2>&1 2>/dev/null)
......
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