template cosmetics

dge_workflow/dge_star_template.sh

@@ -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
 

dge_workflow/star_align.kts

@@ -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(", ")}" }
 }
 

tool_setup.sh

+
 ## 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
 
 
+