User: ole.tange
ole.tange • 3.3k
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Posts by ole.tange
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... If you add an example of how you do it without GNU Parallel, then you may have more luck getting a usable answer. ...
written 25 days ago by
ole.tange • 3.3k
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7 follow
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... [GNU Parallel][1] is often used in bioinformatics.
To make it easier to get started there is now a book. The book "GNU Parallel 2018" is available [in print][2] or [online][3].
If you have never used GNU Parallel, but you are using the command line, then you should consider spending 15 minutes on ...
written 11 weeks ago by
ole.tange • 3.3k
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... Can you elaborate in why you do not have that? Is your reason covered on https://oletange.wordpress.com/2018/03/28/excuses-for-not-installing-gnu-parallel/ ...
written 4 months ago by
ole.tange • 3.3k
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... Can you test if this works, too:
parallel -a ../Big_bed.bed --pipe-part --block -1 --fifo \
annotatePeaks.pl {} hg19 > ./../anno_chunks/{.}_annotated.txt
or this (slower):
parallel -a ../Big_bed.bed --pipe-part --block -1 --cat \
annotatePeaks.pl {} hg19 > ./../anno_chun ...
written 6 months ago by
ole.tange • 3.3k
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657
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... `find` is used because OP used `find`.
Your solution will often give the same result, but will fail if the files are in subdirs inside path_to_fastq or if there are so many that they do not fit on a single command line.
...
written 6 months ago by
ole.tange • 3.3k
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... This:
find path_to_fastq -name "*_R1_001.fastq.gz" |
parallel -j 1 trim_galore --paired --fastqc -o trim_galore/ {} {= s/_R1_/_R2_/ =}
or:
find path_to_fastq -name "*_R1_001.fastq.gz" |
parallel --plus -j 1 trim_galore --paired --fastqc -o trim_galore/ {} {/_R1_/_R2_}
...
written 6 months ago by
ole.tange • 3.3k
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3
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900
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3
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... I have found no way to increase the execve limit. ...
written 7 months ago by
ole.tange • 3.3k
0
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3
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900
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3
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... The problem is in execve, which has the 128KB limit. In other words: It is not the same limit as you see in `getconf ARG_MAX`.
...
written 7 months ago by
ole.tange • 3.3k
5
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3
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900
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... GNU Parallel pessimistically assumes all characters have to be quoted. For this reason the max line length is half of what you would otherwise expect.
> I have a file with the commands to run (several thousand) and I pipe it to parallel. It seems one of these commands is way too big...
A comman ...
written 7 months ago by
ole.tange • 3.3k
0
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10
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105k
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10
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... Use Bash's builtin `printf`. Because it is builtin it is not subject to the same limit:
printf "%s\0" seq.* | parallel do something ...
written 7 months ago by
ole.tange • 3.3k
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created a post with more than 5 votes.
For A: Gnu Parallel Quoting With Awk
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For A: Gnu Parallel Quoting With Awk
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For A: What is the correct way to use GNU parallel with Primer3?
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For A: What is the correct way to use GNU parallel with Primer3?
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For A: What is the correct way to use GNU parallel with Primer3?
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For A: What is the correct way to use GNU parallel with Primer3?
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For Got Multiple Cpus? Activate Them With Gnu Parallel
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For A: Piping With Samtools, Bwa And Bedtools
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For A: Gnu Parallel Quoting With Awk
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For Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
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For Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
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For A: Piping With Samtools, Bwa And Bedtools
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For Got Multiple Cpus? Activate Them With Gnu Parallel
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For C: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
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