User: ole.tange
ole.tange • 3.1k
- Reputation:
- 3,090
- Status:
- Trusted
- Location:
- Denmark
- Last seen:
- 5 days, 2 hours ago
- Joined:
- 5 years, 8 months ago
- Email:
- b***********@tange.dk
about me
Posts by ole.tange
<prev
• 77 results •
page 1 of 8 •
next >
0
votes
2
answers
181
views
2
answers
... I have found no way to increase the execve limit. ...
written 6 days ago by
ole.tange • 3.1k
0
votes
2
answers
181
views
2
answers
... The problem is in execve, which has the 128KB limit. In other words: It is not the same limit as you see in `getconf ARG_MAX`.
...
written 7 days ago by
ole.tange • 3.1k
5
votes
2
answers
181
views
2
answers
... GNU Parallel pessimistically assumes all characters have to be quoted. For this reason the max line length is half of what you would otherwise expect.
> I have a file with the commands to run (several thousand) and I pipe it to parallel. It seems one of these commands is way too big...
A comman ...
written 8 days ago by
ole.tange • 3.1k
0
votes
10
answers
99k
views
10
answers
... Use Bash's builtin `printf`. Because it is builtin it is not subject to the same limit:
printf "%s\0" seq.* | parallel do something ...
written 28 days ago by
ole.tange • 3.1k
0
votes
1
answer
168
views
1
answers
... Or shorter: `ls *_1.fastq.gz | parallel --plus "bwa mem idx.fa {} {%_1.fastq.gz}_2.fastq.gz > {%_1.fastq.gz}.sam"`
...
written 9 weeks ago by
ole.tange • 3.1k
2
votes
10
answers
99k
views
10
answers
... The GNU Parallel 2018 book will be launched on 2018-05-11: https://www.prosa.dk/nc/arrangementer/arrangement/gnu-parallel-foredrag-og-boglancering/
But it can already be gotten at http://www.lulu.com/shop/ole-tange/gnu-parallel-2018/paperback/product-23558902.html
The source for the book is here: ...
written 10 weeks ago by
ole.tange • 3.1k
0
votes
1
answer
317
views
1
answers
... I have not, but I am pretty sure the conclusion will be the same: It depends, and you should therefore test with different parallelization and measure.
...
written 12 weeks ago by
ole.tange • 3.1k
0
votes
1
answer
317
views
1
answers
... See also: https://oletange.wordpress.com/2015/07/04/parallel-disk-io-is-it-faster/ ...
written 12 weeks ago by
ole.tange • 3.1k
4
votes
1
answer
317
views
1
answers
... doit() {
file="$1"
out="$2"
(samtools view -H $file | awk '(/^@SQ/ && /chrM/) || (!/^@SQ/) {print $0} ';
samtools view $file) | samtools view -hb - > $out
}
export -f doit
parallel doit {} {.}_filtered_re-header.bam ::: *.bam
Or if you want to use ...
written 4 months ago by
ole.tange • 3.1k
0
votes
2
answers
720
views
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 11 months ago by
ole.tange • 3.1k
Latest awards to ole.tange
Teacher
7 days 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 months ago,
created an answer with at least 3 up-votes.
For A: What is the correct way to use GNU parallel with Primer3?
Voter
12 months ago,
voted more than 100 times.
Teacher
16 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
2.4 years ago,
created an answer that has been accepted.
For A: What is the correct way to use GNU parallel with Primer3?
Teacher
2.4 years ago,
created an answer with at least 3 up-votes.
For A: What is the correct way to use GNU parallel with Primer3?
Popular Question
3.0 years ago,
created a question with more than 1,000 views.
For Got Multiple Cpus? Activate Them With Gnu Parallel
Good Answer
3.2 years ago,
created an answer that was upvoted at least 5 times.
For A: Piping With Samtools, Bwa And Bedtools
Scholar
3.3 years ago,
created an answer that has been accepted.
For A: What is the correct way to use GNU parallel with Primer3?
Teacher
3.3 years ago,
created an answer with at least 3 up-votes.
For A: Gnu Parallel Quoting With Awk
Appreciated
3.4 years ago,
created a post with more than 5 votes.
For Got Multiple Cpus? Activate Them With Gnu Parallel
Teacher
3.8 years ago,
created an answer with at least 3 up-votes.
For A: Piping With Samtools, Bwa And Bedtools
Popular Question
4.0 years ago,
created a question with more than 1,000 views.
For Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Prophet
4.1 years ago,
created a post with more than 20 followers.
For Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Good Answer
4.1 years ago,
created an answer that was upvoted at least 5 times.
For A: Piping With Samtools, Bwa And Bedtools
Appreciated
4.2 years ago,
created a post with more than 5 votes.
For Got Multiple Cpus? Activate Them With Gnu Parallel
Guru
4.2 years ago,
received more than 100 upvotes.
Supporter
4.2 years ago,
voted at least 25 times.
Teacher
4.2 years ago,
created an answer with at least 3 up-votes.
For A: Piping With Samtools, Bwa And Bedtools
Appreciated
4.5 years ago,
created a post with more than 5 votes.
For Got Multiple Cpus? Activate Them With Gnu Parallel
Commentator
5.4 years ago,
created a comment with at least 3 up-votes.
For C: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Epic Question
5.4 years ago,
created a question with more than 10,000 views.
For Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Gold Standard
5.4 years ago,
created a post with more than 25 bookmarks.
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: 1965 users visited in the last hour