Commit d1800606 authored by Holger Brandl's avatar Holger Brandl

template cosmetics

parent a61995a1
......@@ -3,15 +3,14 @@ export project="TODO define project name"
# screen -R ${project}
## madmax
## cluster
if [ "$HOSTNAME"=="falcon1" ]; then
export PRJ_DATA="/projects/bioinfo/holger/projects/${project}"
export PRJ_SCRIPTS="/projects/bioinfo/holger/scripts/${project}"
export NGS_TOOLS="/projects/bioinfo/scripts/ngs_tools/dev"
## TODO define igenome to be used
## igenome=/projects/bioinfo/igenomes/Canis_familiaris/Ensembl/CanFam3.1
#igenome=<<<<TBD>>>>
## IGENOME=/projects/bioinfo/igenomes/Canis_familiaris/Ensembl/CanFam3.1
fi
## bioinfo
......@@ -19,6 +18,9 @@ if [ $(hostname) == "bioinformatics-srv1" ]; then
export PRJ_DATA=/net/mack/lustre/projects/bioinfo/holger/projects/${project}
export PRJ_SCRIPTS==/net/mack/lustre/projects/bioinfo/holger/scripts/${project}
export NGS_TOOLS=/net/mack/lustre/projects/bioinfo/scripts/ngs_tools/dev
## TODO define igenome to be used
## export IGENOME=/local2/igenomes/Drosophila_melanogaster/Ensembl_81/BDGP6/
fi
......@@ -89,13 +91,14 @@ jl wait --email --report
dge_fastqc $(ls *fastq.gz) &
#zcat *fastq.gz | head
########################################################################################################################
### Alignment the reads
mcdir $PRJ_DATA/alignments
star_align.kts ${igenome} $(ls ${PRJ_DATA}/lanereps_pooled/*.fastq.gz) 2>&1 | tee star_algin.log
star_align.kts ${IGENOME} $(ls ${PRJ_DATA}/lanereps_pooled/*.fastq.gz) 2>&1 | tee star_algin.log
#dge_bam_correlate . & # part of star_align.kts now
......
......@@ -73,8 +73,8 @@ if (!File("${star_index}/SA").isFile())
//println("files are ${fastqFiles.joinToString(", ")}")
// make sure all fastq files do exist (for symlinks see http://www.java2s.com/Code/Java/JDK-7/Isfileasymboliclink.htm
//fastqFiles.filter { !it.isFile }.let {
fastqFiles.filter { !(it.exists() || Files.isSymbolicLink(it.toPath())) }.let {
//fastqFiles.filter { !(it.exists() || Files.isSymbolicLink(it.toPath())) }.let {
fastqFiles.filter { !it.isFile }.let {
require(it.isEmpty()) { "Some fastq files do not exist ${it.map { it.absoluteFile }.joinToString(", ")}" }
}
......
## DeepTools
#cd ~/bin
......@@ -177,17 +178,45 @@ tar xvf sratoolkit.2.8.2-1-ubuntu64.tar.gz
## iGenomes
cd /local2/igenomes
mcdir temp
cd /projects/bioinfo/igenomes
#export NGS_TOOLS=/net/mack/lustre/projects/bioinfo/scripts/ngs_tools/dev
export NGS_TOOLS=/projects/bioinfo/scripts/ngs_tools/dev
source ${NGS_TOOLS}/dge_workflow/dge_utils.sh
#mcdir temp
wget ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/Ensembl/NCBIM37/Mus_musculus_Ensembl_NCBIM37.tar.gz
tar xvf Mus_musculus_Ensembl_NCBIM37.tar.gz
## here: extract annoation version and rename sub-folder accordingly
## here: extract annotation version and rename sub-folder accordingly
## build star index
export NGS_TOOLS=/net/mack/lustre/projects/bioinfo/scripts/ngs_tools/dev
source ${NGS_TOOLS}/dge_workflow/dge_utils.sh
dge_create_star_index /local2/igenomes/Mus_Musculus/Ensembl/NCBIM37__ens66_july2015
## dmel
#cd /local2/igenomes
cd /projects/bioinfo/igenomes
wget ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Drosophila_melanogaster/Ensembl/BDGP6/Drosophila_melanogaster_Ensembl_BDGP6.tar.gz
tar xvf Drosophila_melanogaster_Ensembl_BDGP6.tar.gz
mailme "igenomes dl donw"
## rename according to version in README.txt
mv Drosophila_melanogaster/Ensembl Drosophila_melanogaster/Ensembl_81
dge_create_star_index Drosophila_melanogaster/Ensembl_81/BDGP6
## sync igenomes between bioninfo and cluster
rsync -avs --delete /net/mack/lustre/projects/bioinfo/igenomes/ /local2/igenomes/
mailme "sync done"
chmod -R ugo-w .
########################################################################################################################
cd ~/bin
wget http://data.broadinstitute.org/igv/projects/downloads/igvtools_2.3.91.zip
tar xvf igvtools_2.3.91.zip
......@@ -202,3 +231,4 @@ cd kallisto-0.43.1
./configure
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