Commit fa9b01e3 authored by Lena Hersemann's avatar Lena Hersemann

Merge remote-tracking branch 'origin/master'

parents ea53f611 6d208308
......@@ -104,7 +104,7 @@ dge_fastqc $(ls *fastq.gz) &
#zcat *fastq.gz | head
########################################################################################################################
### Alignment the reads
### Align the reads
mcdir ${PRJ_DATA}/alignments
......
......@@ -47,22 +47,6 @@ source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.39/R/r
source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.39/bash/core_utils.sh 2>&1 2>/dev/null)
## backward compatibility wrappers for old shell cluster utils
#joblist(){
# jl add $*
#}
#export -f joblist
#
#
#wait4jobs(){
# jl wait $*
#}
#export -f wait4jobs
# which tophat; which bowtie2; which cuffdiff
mcdir(){
if [ ! -d "$1" ]; then
mkdir "$1";
......@@ -327,7 +311,8 @@ dge_create_star_index(){
echo "Usage: dge_create_star_index <igenome>" >&2 ; return;
fi
igenome=$1
#igenome="Pan_troglodytes/Ensembl_81/CHIMP2.1.4"
local igenome=$1
if [ ! -d "$igenome" ] | [ ! -d "${igenome}/Sequence" ]; then
echo "igenome directory '$igenome' does not exist" >&2 ; return;
......@@ -347,6 +332,7 @@ dge_create_star_index(){
cmd="STAR --runMode genomeGenerate --genomeDir ${star_index} --genomeFastaFiles ${igenome}/Sequence/WholeGenomeFasta/genome.fa --runThreadN 5"
#eval $cmd
#echo $cmd
#STAR --runMode genomeGenerate --genomeDir ${star_index} --genomeFastaFiles ${igenome}/Sequence/Chromosomes/*.fa --runThreadN 10
jl submit --wait -t 5 -w 10:00 -m 50g -n "${PRJ_NAME}_star_index" "$cmd"
......
......@@ -41,7 +41,11 @@ RUN /bin/bash -c 'source ~/.profile && sdkman_auto_answer=true && sdk install ko
## install kscript
RUN apt-get install -y bc
RUN curl -Lso /bin/kscript https://git.io/v9R73 && chmod u+x /bin/kscript
RUN apt-get install -y git
## todo fix this for v2.X release
#RUN curl -Lso /bin/kscript https://git.io/v9R73 && chmod u+x /bin/kscript
# https://stackoverflow.com/questions/27093612/in-a-dockerfile-how-to-update-path-environment-variable
ENV PATH="~/bin:${PATH}"
......
#bi
cd /net/mack/lustre/projects/bioinfo/holger/scripts/ngs_tools//misc/docker_image/
cd /net/mack/lustre/projects/bioinfo/brandl/scripts/ngs_tools//misc/docker_image/
docker build -t bioinfo_base .
docker run -it bioinfo_base
......
......@@ -197,15 +197,21 @@ picardVersion=2.10.2
wget -O picard_tools/picard_v${picardVersion}.jar -N https://github.com/broadinstitute/picard/releases/download/${picardVersion}/picard.jar
## joblist https://github.com/holgerbrandl/joblist
cd /projects/bioinfo/tools/
curl https://cloud.mpi-cbg.de/index.php/s/hjRbxtxcuhNKlTz/download | tar -zxvf -
########################################################################################################################
## iGenomes
# screen -R igenome_build
cd /projects/bioinfo/igenomes
#export NGS_TOOLS=/net/mack/lustre/projects/bioinfo/brandl/scripts/ngs_tools/
export NGS_TOOLS=/projects/bioinfo/scripts/ngs_tools/dev
export NGS_TOOLS="/projects/bioinfo/$(whoami)/scripts/ngs_tools"
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)
source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.42/bash/core_utils.sh 2>&1 2>/dev/null)
......@@ -231,6 +237,23 @@ mv Drosophila_melanogaster/Ensembl Drosophila_melanogaster/Ensembl_81
dge_create_star_index Drosophila_melanogaster/Ensembl_81/BDGP6
## chimpanzee
wget ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Pan_troglodytes/Ensembl/CHIMP2.1.4/Pan_troglodytes_Ensembl_CHIMP2.1.4.tar.gz
tar xvf Pan_troglodytes_Ensembl_CHIMP2.1.4.tar.gz
## rename according to version in README.txt
cat Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt
mv Pan_troglodytes/Ensembl Pan_troglodytes/Ensembl_81
#cd Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/
#wget ftp://ftp.ensembl.org/pub/release-90/gtf/pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.90.gtf.gz
dge_create_star_index Pan_troglodytes/Ensembl_81/CHIMP2.1.4
mailme "igenomes dl done"
## hsap
chmod +w /projects/bioinfo/igenomes
cd /projects/bioinfo/igenomes/temp
......
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