User: ole.tange

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ole.tange3.6k
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Posts by ole.tange

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Answer: A: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
... **EXAMPLE: Call program with FASTA sequence** FASTA files have the format: ...
written 4 weeks ago by ole.tange3.6k
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Answer: A: Calculating Shannon entropy for RNA sequences in multi-fasta using rnaentropy
... 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 ...
written 4 weeks ago by ole.tange3.6k • updated 4 weeks ago by zx87548.7k
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Answer: A: bwa mem: fail to locate the index files
... 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 4 months ago by ole.tange3.6k
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Answer: A: using GNU parallel for bwa mem and samtools
... 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 "$i ...
written 4 months ago by ole.tange3.6k
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Comment: C: How to extract filename and change text in the same file
... It is covered in GNU Parallel 2018 chapter 5 (Online https://doi.org/10.5281/zenodo.1146014, printed www.lulu.com/shop/ole-tange/gnu-parallel-2018/paperback/product-23558902.html) ...
written 9 months ago by ole.tange3.6k
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Comment: C: How to extract filename and change text in the same file
... Fix: `vc$f` -> `vcf\$`. Also try: `parallel --plus 'sed -i "s|Sample1$|{%.new.vcf}|"' {} ::: *.new.vcf` ...
written 9 months ago by ole.tange3.6k
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Answer: A: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
... GNU Parallel now has a cheat sheet: https://www.gnu.org/software/parallel/parallel_cheat.pdf ...
written 9 months ago by ole.tange3.6k
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Comment: C: How to speed up trimming using trim galorer
... Shorter: parallel --plus 'trim_galore --paired {...}.R1.fq.gz {...}.R2.fq.gz' ::: *R1.fq.gz ...
written 10 months ago by ole.tange3.6k
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Comment: C: How to run SNPEff jar for a batch of VCF files using GNU parallel tool?
... If you add an example of how you do it without GNU Parallel, then you may have more luck getting a usable answer. ...
written 11 months ago by ole.tange3.6k
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7 follow
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Tool: Book: GNU Parallel 2018 - for beginners and advanced users
... [GNU Parallel][1] is often used in bioinformatics. To make it easier to get started there is now a book. The book "GNU Parallel 2018" is available [in print][2] or [online][3]. If you have never used GNU Parallel, but you are using the command line, then you should consider spending 15 minutes on ...
ngs parallel tool written 13 months ago by ole.tange3.6k

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Appreciated 5 days ago, created a post with more than 5 votes. For A: Gnu Parallel Quoting With Awk
Good Answer 26 days ago, created an answer that was upvoted at least 5 times. For A: Gnu Parallel Quoting With Awk
Appreciated 4 weeks ago, created a post with more than 5 votes. For A: Gnu Parallel Quoting With Awk
Teacher 4 weeks 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?
Scholar 4 months ago, created an answer that has been accepted. For A: What is the correct way to use GNU parallel with Primer3?
Commentator 5 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 6 months ago, created an answer that was upvoted at least 5 times. For A: Gnu Parallel Quoting With Awk
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Teacher 9 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 13 months ago, created a post with more than 5 votes. For A: Gnu Parallel Quoting With Awk
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Teacher 18 months ago, created an answer with at least 3 up-votes. For A: What is the correct way to use GNU parallel with Primer3?
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Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: What is the correct way to use GNU parallel with Primer3?
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Popular Question 4.5 years ago, created a question with more than 1,000 views. For Got Multiple Cpus? Activate Them With Gnu Parallel
Good Answer 4.7 years ago, created an answer that was upvoted at least 5 times. For A: Piping With Samtools, Bwa And Bedtools
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: Gnu Parallel Quoting With Awk
Scholar 4.7 years ago, created an answer that has been accepted. For A: What is the correct way to use GNU parallel with Primer3?
Appreciated 4.9 years ago, created a post with more than 5 votes. For Got Multiple Cpus? Activate Them With Gnu Parallel
Teacher 5.3 years ago, created an answer with at least 3 up-votes. For A: Piping With Samtools, Bwa And Bedtools
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them

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