User: ole.tange
ole.tange • 3.6k
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Posts by ole.tange
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... **EXAMPLE: Call program with FASTA sequence**
FASTA files have the format: ...
written 4 weeks ago by
ole.tange • 3.6k
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... With GNU Parallel (https://www.biostars.org/p/63816/) you would do:
cat in.fasta |
parallel --pipe -N1 --recstart '>' --rrs 'read a; echo Doing "$a"; ./RNAentropy -s $(tr -d "\n")'
From [GNU Parallel Tutorial: Informational](https://www.gnu.org/software/parallel/parallel_tutoria ...
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... GNU Parallel does not run its jobs in the same shell session as it is started. That means that non-exported variables and non-exported functions cannot be seen.
However, `env_parallel` can make a copy of the environment in the current session and pass that to GNU Parallel. By using `env_parallel -- ...
written 4 months ago by
ole.tange • 3.6k
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... It makes it easier to read and to test if you create a function and call that.
You can then test your function on a single file set before handing it to GNU Parallel:
bwatosam() {
id="$1"
bwa mem -t 10 -M -R "@RG\tID:{}\tSM:{}\tPL:ILLUMINA\tLB:{}" hg1kv37.fa "$id"_R1.fq.gz "$i ...
written 4 months ago by
ole.tange • 3.6k
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... It is covered in GNU Parallel 2018 chapter 5 (Online https://doi.org/10.5281/zenodo.1146014, printed www.lulu.com/shop/ole-tange/gnu-parallel-2018/paperback/product-23558902.html) ...
written 9 months ago by
ole.tange • 3.6k
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... Fix: `vc$f` -> `vcf\$`.
Also try: `parallel --plus 'sed -i "s|Sample1$|{%.new.vcf}|"' {} ::: *.new.vcf` ...
written 9 months ago by
ole.tange • 3.6k
2
votes
12
answers
113k
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12
answers
... GNU Parallel now has a cheat sheet:
https://www.gnu.org/software/parallel/parallel_cheat.pdf ...
written 9 months ago by
ole.tange • 3.6k
2
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2
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876
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2
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... Shorter:
parallel --plus 'trim_galore --paired {...}.R1.fq.gz {...}.R2.fq.gz' ::: *R1.fq.gz ...
written 10 months ago by
ole.tange • 3.6k
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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 11 months ago by
ole.tange • 3.6k
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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 13 months ago by
ole.tange • 3.6k
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