User: ole.tange
ole.tange • 3.7k
- Reputation:
- 3,700
- Status:
- Trusted
- Location:
- Denmark
- Last seen:
- 1 month, 1 week ago
- Joined:
- 7 years, 5 months ago
- Email:
- b***********@tange.dk
about me
Posts by ole.tange
<prev
• 92 results •
page 1 of 10 •
next >
0
votes
6
answers
225
views
6
answers
... parallel --dry-run mv {} '{=s/GEN\d+_N_(\w+)_lib\d+_\d+_(\d+_R\d)/$1_$2/=}' ::: *.fastq ...
written 6 weeks ago by
ole.tange • 3.7k
0
votes
12
answers
115k
views
12
answers
... **EXAMPLE: Call program with FASTA sequence**
FASTA files have the format: ...
written 4 months ago by
ole.tange • 3.7k
6
votes
2
answers
268
views
2
answers
... With GNU Parallel (https://www.biostars.org/p/63816/) you would do:
cat in.fasta |
parallel --pipe -N1 --recstart '>' --rrs 'read a; echo Doing "$a"; ./RNAentropy -s $(tr -d "\n")'
From [GNU Parallel Tutorial: Informational](https://www.gnu.org/software/parallel/parallel_tutoria ...
1
vote
2
answers
496
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 8 months ago by
ole.tange • 3.7k
3
votes
1
answer
422
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 "$i ...
written 8 months ago by
ole.tange • 3.7k
0
votes
2
answers
635
views
2
answers
... It is covered in GNU Parallel 2018 chapter 5 (Online https://doi.org/10.5281/zenodo.1146014, printed www.lulu.com/shop/ole-tange/gnu-parallel-2018/paperback/product-23558902.html) ...
written 13 months ago by
ole.tange • 3.7k
0
votes
2
answers
635
views
2
answers
... Fix: `vc$f` -> `vcf\$`.
Also try: `parallel --plus 'sed -i "s|Sample1$|{%.new.vcf}|"' {} ::: *.new.vcf` ...
written 13 months ago by
ole.tange • 3.7k
2
votes
12
answers
115k
views
12
answers
... GNU Parallel now has a cheat sheet:
https://www.gnu.org/software/parallel/parallel_cheat.pdf ...
written 13 months ago by
ole.tange • 3.7k
2
votes
2
answers
1.3k
views
2
answers
... Shorter:
parallel --plus 'trim_galore --paired {...}.R1.fq.gz {...}.R2.fq.gz' ::: *R1.fq.gz ...
written 14 months ago by
ole.tange • 3.7k
0
votes
0
answers
979
views
0
answers
... If you add an example of how you do it without GNU Parallel, then you may have more luck getting a usable answer. ...
written 15 months ago by
ole.tange • 3.7k
Latest awards to ole.tange
Appreciated
4 months ago,
created a post with more than 5 votes.
For A: Gnu Parallel Quoting With Awk
Good Answer
4 months ago,
created an answer that was upvoted at least 5 times.
For A: Gnu Parallel Quoting With Awk
Appreciated
5 months ago,
created a post with more than 5 votes.
For A: Gnu Parallel Quoting With Awk
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: What is the correct way to use GNU parallel with Primer3?
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: What is the correct way to use GNU parallel with Primer3?
Scholar
8 months ago,
created an answer that has been accepted.
For A: What is the correct way to use GNU parallel with Primer3?
Commentator
9 months ago,
created a comment with at least 3 up-votes.
For C: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Good Answer
10 months ago,
created an answer that was upvoted at least 5 times.
For A: Gnu Parallel Quoting With Awk
Appreciated
10 months ago,
created a post with more than 5 votes.
For A: Gnu Parallel Quoting With Awk
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: What is the correct way to use GNU parallel with Primer3?
Appreciated
17 months ago,
created a post with more than 5 votes.
For A: Gnu Parallel Quoting With Awk
Appreciated
21 months ago,
created a post with more than 5 votes.
For A: Gnu Parallel Quoting With Awk
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: What is the correct way to use GNU parallel with Primer3?
Teacher
2.1 years ago,
created an answer with at least 3 up-votes.
For A: What is the correct way to use GNU parallel with Primer3?
Voter
2.8 years ago,
voted more than 100 times.
Teacher
3.1 years ago,
created an answer with at least 3 up-votes.
For A: What is the correct way to use GNU parallel with Primer3?
Teacher
4.2 years ago,
created an answer with at least 3 up-votes.
For A: What is the correct way to use GNU parallel with Primer3?
Scholar
4.2 years ago,
created an answer that has been accepted.
For A: What is the correct way to use GNU parallel with Primer3?
Popular Question
4.8 years ago,
created a question with more than 1,000 views.
For Got Multiple Cpus? Activate Them With Gnu Parallel
Good Answer
5.0 years ago,
created an answer that was upvoted at least 5 times.
For A: Piping With Samtools, Bwa And Bedtools
Teacher
5.0 years ago,
created an answer with at least 3 up-votes.
For A: Gnu Parallel Quoting With Awk
Scholar
5.0 years ago,
created an answer that has been accepted.
For A: What is the correct way to use GNU parallel with Primer3?
Appreciated
5.2 years ago,
created a post with more than 5 votes.
For Got Multiple Cpus? Activate Them With Gnu Parallel
Teacher
5.6 years ago,
created an answer with at least 3 up-votes.
For A: Piping With Samtools, Bwa And Bedtools
Popular Question
5.8 years ago,
created a question with more than 1,000 views.
For Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1676 users visited in the last hour