User: ole.tange
ole.tange • 3.9k
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Posts by ole.tange
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3
votes
2
answers
142
views
2
answers
... @Pierre's and @Wouter's solutions should work for you.
The problem is that this:
parallel bcftools stats chr{}.bcf | grep "number of records:" | cut -f 4 > chr{}.txt ::: {1..22}
is interpreted as this:
parallel bcftools stats chr{}.bcf |
grep "number of records:" |
cut -f ...
written 17 days ago by
ole.tange • 3.9k
3
votes
2
answers
296
views
2
answers
... parallel --plus "command -t {1} {2} {3} > {1}_{2/..}.out " ::: 4 8 ::: File1 File3 :::+ File2 File4 ...
written 3 months ago by
ole.tange • 3.9k
0
votes
2
answers
2.5k
views
2
answers
... No need for `wait`. GNU Parallel does that for you. ...
written 3 months ago by
ole.tange • 3.9k
2
votes
1
answer
191
views
1
answers
... Something like this:
IDLIST=IDLIST
mysearch() {
query="$1"
IFS=$'\n'
for hit in $(esearch -db sra -query "$query" |
efetch --format runinfo |
grep SRR); do
echo "$query,${hit}"
done
}
...
written 4 months ago by
ole.tange • 3.9k
1
vote
3
answers
329
views
3
answers
... Make a function that takes a dir and the base filename as argument:
doit() {
dir="$1"
f="$2"
cd "$dir"
echo "Processing sample $f"
salmon quant -i gencode.v33.transcripts.index -l A -1 ${f}_1.fq.gz -2 ${f}_2.fq.gz -p 6 --gcBias --validateMappings -o quants/${f}_qua ...
written 4 months ago by
ole.tange • 3.9k
0
votes
6
answers
637
views
6
answers
... parallel --dry-run mv {} '{=s/GEN\d+_N_(\w+)_lib\d+_\d+_(\d+_R\d)/$1_$2/=}' ::: *.fastq ...
written 9 months ago by
ole.tange • 3.9k
0
votes
8
answers
121k
views
8
answers
... **EXAMPLE: Call program with FASTA sequence**
FASTA files have the format: ...
written 13 months ago by
ole.tange • 3.9k
7
votes
2
answers
493
views
2
answers
... With GNU Parallel (https://www.biostars.org/p/63816/) you would do:
cat in.fasta |
parallel --pipe -N1 --recstart '>' --rrs 'read a; echo Doing "$a"; ./RNAentropy -s $(tr -d "\n")'
From [GNU Parallel Tutorial: Informational](https://www.gnu.org/software/parallel/parallel_tutoria ...
1
vote
2
answers
1.2k
views
2
answers
... 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 16 months ago by
ole.tange • 3.9k
3
votes
1
answer
737
views
1
answers
... 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 16 months ago by
ole.tange • 3.9k
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