User: ole.tange
ole.tange • 3.4k
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Posts by ole.tange
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... It is covered in GNU Parallel 2018 chapter 5 (Online https://doi.org/10.5281/zenodo.1146014, printed www.lulu.com/shop/ole-tange/gnu-parallel-2018/paperback/product-23558902.html) ...
written 11 days ago by
ole.tange • 3.4k
0
votes
2
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178
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2
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... Fix: `vc$f` -> `vcf\$`.
Also try: `parallel --plus 'sed -i "s|Sample1$|{%.new.vcf}|"' {} ::: *.new.vcf` ...
written 14 days ago by
ole.tange • 3.4k
2
votes
11
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107k
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11
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... GNU Parallel now has a cheat sheet:
https://www.gnu.org/software/parallel/parallel_cheat.pdf ...
written 16 days ago by
ole.tange • 3.4k
2
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2
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248
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... Shorter:
parallel --plus 'trim_galore --paired {...}.R1.fq.gz {...}.R2.fq.gz' ::: *R1.fq.gz ...
written 9 weeks ago by
ole.tange • 3.4k
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535
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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 3 months ago by
ole.tange • 3.4k
12
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416
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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 4 months ago by
ole.tange • 3.4k
0
votes
1
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372
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1
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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 6 months ago by
ole.tange • 3.4k
0
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2
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340
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2
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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 8 months ago by
ole.tange • 3.4k
0
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1
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896
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1
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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 8 months ago by
ole.tange • 3.4k
1
vote
1
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896
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1
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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 8 months ago by
ole.tange • 3.4k
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