Commit 1d27db8d authored by nchernia's avatar nchernia
Browse files

got rid of bc dependency

parent cae9b79a

AWS/scripts/juicer.sh

+1 −1
Changes for AWS/scripts/juicer.sh: 1 added line, 1 removed line.
Original line number Diff line number Diff line
@@ -124,7 +124,7 @@ shortHelp2="* [end]: use the short read aligner on read end, must be one of 1 or 
stageHelp="* [stage]: must be one of \"merge\", \"dedup\", \"final\", \"postproc\", or \"early\".\n    -Use \"merge\" when alignment has finished but the merged_sort file has not\n     yet been created.\n    -Use \"dedup\" when the files have been merged into merged_sort but\n     merged_nodups has not yet been created.\n    -Use \"final\" when the reads have been deduped into merged_nodups but the\n     final stats and hic files have not yet been created.\n    -Use \"postproc\" when the hic files have been created and only\n     postprocessing feature annotation remains to be completed.\n    -Use \"early\" for an early exit, before the final creation of the stats and\n     hic files"

pathHelp="* [chrom.sizes path]: enter path for chrom.sizes file"

siteFileHelp="* [restriction site file]: enter path for restriction site file (locations of\n  restriction sites in genome; can be generated with the script\n  misc/generate_site_positions.py)"

chunkHelp="* [chunk size]: number of lines in split files, must be multiple of 4\n  (default ${splitsize}, which equals $(echo "scale=1; ${splitsize}/4000000" | bc) million reads)"

chunkHelp="* [chunk size]: number of lines in split files, must be multiple of 4\n  (default ${splitsize}, which equals $(awk -v ss=${splitsize} 'BEGIN{print ss/4000000}') million reads)"

scriptDirHelp="* [Juicer scripts directory]: set the Juicer directory,\n  which should have scripts/ references/ and restriction_sites/ underneath it\n  (default ${juiceDir})"

refSeqHelp="* [reference genome file]: enter path for reference sequence file, BWA index\n  files must be in same directory"

queueTimeHelp="* [queue time limit]: time limit for queue, i.e. -W 12:00 is 12 hours\n  (default ${queue_time})"

LSF/scripts/juicer.sh

+1 −1
Changes for LSF/scripts/juicer.sh: 1 added line, 1 removed line.
Original line number Diff line number Diff line
@@ -125,7 +125,7 @@ shortHelp2="* [end]: use the short read aligner on read end, must be one of 1 or 
stageHelp="* [stage]: must be one of \"merge\", \"dedup\", \"final\", \"postproc\", or \"early\".\n    -Use \"merge\" when alignment has finished but the merged_sort file has not\n     yet been created.\n    -Use \"dedup\" when the files have been merged into merged_sort but\n     merged_nodups has not yet been created.\n    -Use \"final\" when the reads have been deduped into merged_nodups but the\n     final stats and hic files have not yet been created.\n    -Use \"postproc\" when the hic files have been created and only\n     postprocessing feature annotation remains to be completed.\n    -Use \"early\" for an early exit, before the final creation of the stats and\n     hic files"

pathHelp="* [chrom.sizes path]: enter path for chrom.sizes file"

siteFileHelp="* [restriction site file]: enter path for restriction site file (locations of\n  restriction sites in genome; can be generated with the script\n  misc/generate_site_positions.py)"

chunkHelp="* [chunk size]: number of lines in split files, must be multiple of 4\n  (default ${splitsize}, which equals $(echo "scale=1; ${splitsize}/4000000" | bc) million reads)"

chunkHelp="* [chunk size]: number of lines in split files, must be multiple of 4\n  (default ${splitsize}, which equals $(awk -v ss=${splitsize} 'BEGIN{print ss/4000000}') million reads)"

scriptDirHelp="* [Juicer scripts directory]: set the Juicer directory,\n  which should have scripts/ references/ and restriction_sites/ underneath it\n  (default ${juiceDir})"

refSeqHelp="* [reference genome file]: enter path for reference sequence file, BWA index\n  files must be in same directory"

queueTimeHelp="* [queue time limit]: time limit for queue, i.e. -W 12:00 is 12 hours\n  (default ${queue_time})"

SLURM/scripts/juicer.sh

+1 −1
Changes for SLURM/scripts/juicer.sh: 1 added line, 1 removed line.
Original line number Diff line number Diff line
@@ -128,7 +128,7 @@ shortHelp2="* [end]: use the short read aligner on read end, must be one of 1 or 
stageHelp="* [stage]: must be one of \"merge\", \"dedup\", \"final\", \"postproc\", or \"early\".\n    -Use \"merge\" when alignment has finished but the merged_sort file has not\n     yet been created.\n    -Use \"dedup\" when the files have been merged into merged_sort but\n     merged_nodups has not yet been created.\n    -Use \"final\" when the reads have been deduped into merged_nodups but the\n     final stats and hic files have not yet been created.\n    -Use \"postproc\" when the hic files have been created and only\n     postprocessing feature annotation remains to be completed.\n    -Use \"early\" for an early exit, before the final creation of the stats and\n     hic files"

pathHelp="* [chrom.sizes path]: enter path for chrom.sizes file"

siteFileHelp="* [restriction site file]: enter path for restriction site file (locations of\n  restriction sites in genome; can be generated with the script\n  misc/generate_site_positions.py)"

chunkHelp="* [chunk size]: number of lines in split files, must be multiple of 4\n  (default ${splitsize}, which equals $(echo "scale=1; ${splitsize}/4000000" | bc) million reads)"

chunkHelp="* [chunk size]: number of lines in split files, must be multiple of 4\n  (default ${splitsize}, which equals $(awk -v ss=${splitsize} 'BEGIN{print ss/4000000}') million reads)"

scriptDirHelp="* [Juicer scripts directory]: set the Juicer directory,\n  which should have scripts/ references/ and restriction_sites/ underneath it\n  (default ${juiceDir})"

refSeqHelp="* [reference genome file]: enter path for reference sequence file, BWA index\n  files must be in same directory"

queueTimeHelp="* [queue time limit]: time limit for queue, i.e. -W 12:00 is 12 hours\n  (default ${queue_time})"

UGER/scripts/juicer.sh

+1 −1
Changes for UGER/scripts/juicer.sh: 1 added line, 1 removed line.
Original line number Diff line number Diff line
@@ -126,7 +126,7 @@ shortHelp2="* [end]: use the short read aligner on read end, must be one of 1 or 
stageHelp="* [stage]: must be one of \"merge\", \"dedup\", \"final\", \"postproc\", or \"early\".\n    -Use \"merge\" when alignment has finished but the merged_sort file has not\n     yet been created.\n    -Use \"dedup\" when the files have been merged into merged_sort but\n     merged_nodups has not yet been created.\n    -Use \"final\" when the reads have been deduped into merged_nodups but the\n     final stats and hic files have not yet been created.\n    -Use \"postproc\" when the hic files have been created and only\n     postprocessing feature annotation remains to be completed.\n    -Use \"early\" for an early exit, before the final creation of the stats and\n     hic files"

pathHelp="* [chrom.sizes path]: enter path for chrom.sizes file"

siteFileHelp="* [restriction site file]: enter path for restriction site file (locations of\n  restriction sites in genome; can be generated with the script\n  misc/generate_site_positions.py)"

chunkHelp="* [chunk size]: number of lines in split files, must be multiple of 4\n  (default ${splitsize}, which equals $(echo "scale=1; ${splitsize}/4000000" | bc) million reads)"

chunkHelp="* [chunk size]: number of lines in split files, must be multiple of 4\n  (default ${splitsize}, which equals $(awk -v ss=${splitsize} 'BEGIN{print ss/4000000}') million reads)"

scriptDirHelp="* [Juicer scripts directory]: set the Juicer directory,\n  which should have scripts/ references/ and restriction_sites/ underneath it\n  (default ${juiceDir})"

refSeqHelp="* [reference genome file]: enter path for reference sequence file, BWA index\n  files must be in same directory"

queueTimeHelp="* [queue time limit]: time limit for queue, i.e. -W 12:00 is 12 hours\n  (default ${queue_time})"

CRA Git | Maintained and supported by SUSTech CRA and CCSE