post processing started

encode-wrapper/get_encode_resources.sh

@@ -24,6 +24,12 @@ ifNotThenWgetAndUntar(){
 ifNotThenWget https://github.com/broadinstitute/cromwell/releases/download/34/cromwell-34.jar
 chmod +rx cromwell-34.jar
 
+ifNotThenWget http://www.epigenomes.ca/resources/GSCtools/BAM2WIG-1.0.0.jar
+
+ifNotThenWget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig 
+chmod +x ./wigToBigWig
+
+
 ifNotThenWgetAndUntar https://storage.googleapis.com/encode-pipeline-genome-data/test_genome_database_hg38_chip.tar
 
 ifNotThenWgetAndUntar https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR936XTK/ENCSR936XTK_fastq_subsampled.tar

encode-wrapper/postprocesstracks

@@ -0,0 +1,17 @@
+#!/bin/bash
+set -eufx -o pipefail
+
+
+mode=""
+bamfile=""
+bindpaths="$PWD"
+bam2wigopts=""
+bam2wigsamtools="-samtools /usr/local/bin/samtools"
+chromsize=""
+
+strippedbam="$(dirname $bamfile)/$(basename $bamfile bam).stripped.bam"
+#/usr/local/bin/samtools view -h $bamfile > $strippedbam
+
+
+chipimage="images/chip_seq_pipeline_v1_1_4-sambamba-0_7_1-rev1.sif"
+singularity exec --cleanenv -B $bindpaths $chipimage java -jar ./BAM2WIG-1.0.0.jar -h  $bam2wigsamtools

initpipe

@@ -4,7 +4,8 @@ set -eufx -o pipefail
 
 cd encode-wrapper
 chmod +x ./get_encode_resources.sh
-./get_encode_resources.sh &> get_encode_resources.log
-python chip.py -get &> chip_get.log
-python  chip.py -pullimage -bindpwd &> chip_pull_image.log
-#apy chip.py -pullimage -bindpwd $PWD/v2/ihec &> chip_pull_image.log
+./get_encode_resources.sh &> ../get_encode_resources.log
+python chip.py -get &> ../chip_get.log
+python  chip.py -pullimage &> ../chip_pull_image.log
+
+chmod ugo+x ./*sh