User: ole.tange
ole.tange • 2.8k
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Posts by ole.tange
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2
answers
166
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2
answers
... It is unclear to me what SRAIdFromPythonInput.txt contains. Can you give a couple of lines as example?
doit() {
i="$1"
echo "$i"
./fastq-dump --split-files $i -v
}
export -f doit
parallel doit :::: SRAIdFromPythonInput.txt
...
written 21 days ago by
ole.tange • 2.8k
0
votes
3
answers
191
views
3
answers
... doit() {
k="$1"
n="$2"
python /home/ubuntu/bin/fastStructure/structure.py -K "$k" --input=../file.snps --output=snpl525D-"$k"-"$n" --format=str
}
export -f doit
parallel doit ::: {1..10} ::: {1..15}
...
written 22 days ago by
ole.tange • 2.8k
0
votes
9
answers
87k
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9
answers
... You should use which ever works faster for you. ...
written 5 weeks ago by
ole.tange • 2.8k
2
votes
5
answers
308
views
5
answers
Comment:
C: Run Samtools on multiple files
... --eta implies --progress, so --progress is not needed. Also try the newer --bar. If you want one per cpu core, leave out -j8. ...
written 7 weeks ago by
ole.tange • 2.8k
1
vote
2
answers
300
views
2
answers
... See https://www.gnu.org/software/parallel/ under "Community maintained packages".
Or use'the 10 second installation:
(wget -O - pi.dk/3 || curl pi.dk/3/ || fetch -o - http://pi.dk/3) | bash
See more on: https://www.biostars.org/p/63816/ ...
written 5 months ago by
ole.tange • 2.8k
2
votes
2
answers
300
views
2
answers
... GNU Parallel solutions:
parallel cat {1} {2} '>' {=1 s/_mapped// =} ::: *_mapped.fq :::+ *_unmapped.fq
parallel --xapply cat {1} {2} '>' {=1 s/_mapped// =} ::: *_mapped.fq ::: *_unmapped.fq
parallel cat {} {= s/_unmapped/_mapped/ =} '>' {= s/_unmapped// =} ::: *_unmapped.fq
...
written 5 months ago by
ole.tange • 2.8k
2
votes
3
answers
256
views
3
answers
... Since 20140722 you can let GNU Parallel do the trimming of the file name:
s/_R..fastq.gz//; will remove _R1.fastq.gz or _R2.fastq.gz
$seen{$_}++ && $job->skip(); will skip the job if the trimmed name is already seen
--rpl '{_} [...]' will replace {_} with [...].
So in tot ...
written 6 months ago by
ole.tange • 2.8k
1
vote
4
answers
389
views
4
answers
... Using GNU Parallel:
parallel variant_calling_cmd {} ::: */*.bam
Learn more:
https://www.biostars.org/p/63816/
...
written 8 months ago by
ole.tange • 2.8k
1
vote
1
answer
295
views
1
answers
... I assume you can run:
my.py fasta/protein314.fa profile/protein314.profile
I also assume that the dir `fasta` and the dir `profile` contains nothing else and that the corresponding files are named the same
parallel my.py ::: fasta/* :::+ profile/*
The :::+ requires a fairly recent versio ...
written 8 months ago by
ole.tange • 2.8k
0
votes
1
answer
524
views
1
answers
... parallel trim_galore --illumina --paired --fastqc -o trim_galore/ {} {=s/_R1_/_R2_/=} ::: *_R1_merged.fastq.gz
...
written 10 months ago by
ole.tange • 2.8k
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