User: ole.tange

gravatar for ole.tange
ole.tange2.8k
Reputation:
2,790
Status:
Trusted
Location:
Denmark
Last seen:
2 weeks, 3 days ago
Joined:
5 years ago
Email:
b***********@tange.dk

about me

Posts by ole.tange

<prev • 68 results • page 1 of 7 • next >
0
votes
2
answers
243
views
2
answers
Answer: A: How to parallelize fastq-dump command when reading SRA IDs from a .txt file?
... 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 12 weeks ago by ole.tange2.8k
0
votes
3
answers
261
views
3
answers
Answer: A: how to run STRUCTURE command n times for each K value?
... 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 12 weeks ago by ole.tange2.8k
0
votes
9
answers
89k
views
9
answers
Comment: C: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
... You should use which ever works faster for you. ...
written 3 months ago by ole.tange2.8k
2
votes
5
answers
460
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 3 months ago by ole.tange2.8k
1
vote
2
answers
371
views
2
answers
Comment: C: How to combine pair end multiple fastq raw read file
... 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 7 months ago by ole.tange2.8k
2
votes
2
answers
371
views
2
answers
Answer: A: How to combine pair end multiple fastq raw read file
... 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 7 months ago by ole.tange2.8k
2
votes
3
answers
296
views
3
answers
Answer: A: How samplelist.txt may look like for parallel
... 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 8 months ago by ole.tange2.8k
1
vote
4
answers
460
views
4
answers
Answer: A: Bash loop for files in several directories
... Using GNU Parallel: parallel variant_calling_cmd {} ::: */*.bam Learn more: https://www.biostars.org/p/63816/ ...
written 10 months ago by ole.tange2.8k
1
vote
1
answer
327
views
1
answers
Answer: A: Run Prediction program on entire folder.
... 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 10 months ago by ole.tange2.8k
1
vote
1
answer
718
views
1
answers
Answer: A: TrimGalore! on multiple paired fastq files
... parallel trim_galore --illumina --paired --fastqc -o trim_galore/ {} {=s/_R1_/_R2_/=} ::: *_R1_merged.fastq.gz ...
written 12 months ago by ole.tange2.8k

Latest awards to ole.tange

Voter 4 months ago, voted more than 100 times.
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 21 months ago, created an answer that has been accepted. For A: What is the correct way to use GNU parallel with Primer3?
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?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Got Multiple Cpus? Activate Them With Gnu Parallel
Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For A: Piping With Samtools, Bwa And Bedtools
Scholar 2.6 years ago, created an answer that has been accepted. For A: What is the correct way to use GNU parallel with Primer3?
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Gnu Parallel Quoting With Awk
Appreciated 2.7 years ago, created a post with more than 5 votes. For Got Multiple Cpus? Activate Them With Gnu Parallel
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Piping With Samtools, Bwa And Bedtools
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Prophet 3.4 years ago, created a post with more than 20 followers. For Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Good Answer 3.4 years ago, created an answer that was upvoted at least 5 times. For A: Piping With Samtools, Bwa And Bedtools
Appreciated 3.5 years ago, created a post with more than 5 votes. For Got Multiple Cpus? Activate Them With Gnu Parallel
Guru 3.5 years ago, received more than 100 upvotes.
Supporter 3.5 years ago, voted at least 25 times.
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Piping With Samtools, Bwa And Bedtools
Appreciated 3.9 years ago, created a post with more than 5 votes. For Got Multiple Cpus? Activate Them With Gnu Parallel
Appreciated 4.1 years ago, created a post with more than 5 votes. For Gnu Parallel Tutorial
Commentator 4.7 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 4.7 years ago, created a question with more than 10,000 views. For Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Gold Standard 4.7 years ago, created a post with more than 25 bookmarks. For Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Great Question 4.7 years ago, created a question with more than 5,000 views. For Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Appreciated 4.7 years ago, created a post with more than 5 votes. For Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 742 users visited in the last hour