Commit 7c63e7cd authored by Holger Brandl's avatar Holger Brandl

added chimp genome

parent 76b09f2b
......@@ -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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