Merge branch 'master' of git.ecdf.ed.ac.uk:igmmbioinformatics/trio-whole-exome

docs/SOP_alignment_variant_annotation.md

@@ -18,12 +18,10 @@ To generate the target BED file, first copy the file Twist_Exome_RefSeq_targets_
 
 ```
 cd /home/u035/project/resources
+source ../scripts/trio_whole_exome_config.sh
 
-../software/bcbio/bin/bedtools slop -g \
-  ../software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa.fai \
-  -i Twist_Exome_RefSeq_targets_hg38.bed -b 15 | \
-  ../software/bcbio/bin/bedtools merge > \
-  Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
+bedtools slop -g $REFERENCE_GENOME.fai -i Twist_Exome_RefSeq_targets_hg38.bed -b 15 | \
+  bedtools merge > Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
 ```
 
 ## Input
@@ -96,7 +94,7 @@ OUTPUT_DIR=$BASE/output
 
 ARCHIVE_DIR=/archive/u035/trio_whole_exome
 
-export PATH=/home/u035/project/software/bcbio/bin:$PATH
+export PATH=/home/u035/project/software/bcbio/tools/bin:$PATH
 ````
 
 ## Template for bcbio configuration

docs/SOP_archiving.md

@@ -8,7 +8,7 @@ The user will need an account on the EPCC Ultra system. Contact Donald Scobbie (
 
 ## Software requirements
 
-Htslib 1.9 and Samtools 1.9 are installed at /home/u035/project/software/bcbio/bin.
+Htslib 1.9 and Samtools 1.9 are installed at /home/u035/project/software/bcbio/tools/bin.
 
 ## Data requirements
 

docs/SOP_sample_transfer_from_EdGe_to_EPCC.md

@@ -22,7 +22,7 @@ This script will be referred to as <user_transfer_info_file>.
 
 ## Software requirements
 
-The Aspera command line interface software (version 3.7.4.147727) is installed in the project area at /home/u035/project/software/aspera/connect/bin. Md5 checksums are calculated by the system function md5sum. GNU Parallels is installed at /home/u035/project/software/bin.
+The Aspera command line interface software (version 3.7.4.147727) is installed in the project area at /home/u035/project/software/aspera/connect/bin. Md5 checksums are calculated by the system function md5sum.
 
 ## Notes
 
@@ -49,7 +49,7 @@ a.	The script is set to request 24 hours of wall time. The transfer speed is rou
 b.	If a download does not complete, this step may be run again and the download will resume from where it left off. If there are any files with extension .partial in the target directory, the download did not complete.
 
 ```
-cd /home/u035/project/trio_whole_exome/logs
+cd /scratch/u035/project/trio_whole_exome/logs
 project_id=<EdGE_project_id>
 transfer_sh=<full_path_to_user_transfer_info_file>
 qsub -v TRANSFER_INFO_FILE=$transfer_sh,PROJECT=$project_id \
@@ -68,7 +68,7 @@ If any files in a download do not have the correct md5 checksum, manually delete
 5. Clean up the logs directory.
 
 ```
-cd /home/u035/project/trio_whole_exome/logs
+cd /scratch/u035/project/trio_whole_exome/logs
 mv aspera.$project_id.* complete/
 mv project/$project_id.log complete/
 ```

docs/Software_installation.md

@@ -15,7 +15,7 @@ wget https://raw.github.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_ins
 ulimit -n 4096
 
 python bcbio_nextgen_install.py /home/u035/project/software/bcbio \
-  --tooldir /home/u035/project/software/bcbio/bin \
+  --tooldir /home/u035/project/software/bcbio/tools \
   --genomes hg38 --aligners bwa \
   --datatarget variation --datatarget gnomad \
   --datatarget vep --datatarget dbnsfp --cores 32 &> bcbio_install_YYYYMMDDhhmm.log