User: ole.tange

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ole.tange3.9k
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Posts by ole.tange

<prev • 96 results • page 1 of 10 • next >
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Answer: A: GNU parallel command with several multiple arguments
... parallel --plus "command -t {1} {2} {3} > {1}_{2/..}.out " ::: 4 8 ::: File1 File3 :::+ File2 File4 ...
written 5 weeks ago by ole.tange3.9k
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Comment: C: Bulk download of entire BioProject SRA
... No need for `wait`. GNU Parallel does that for you. ...
written 6 weeks ago by ole.tange3.9k
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Answer: A: How to set sleep in GNU parallel in a esearch/efetch script
... 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 6 weeks ago by ole.tange3.9k
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Answer: A: How do I use bash loop to map with Salmon on files in multiple folders
... 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 9 weeks ago by ole.tange3.9k
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Comment: C: How to rename multiple fastq files
... parallel --dry-run mv {} '{=s/GEN\d+_N_(\w+)_lib\d+_\d+_(\d+_R\d)/$1_$2/=}' ::: *.fastq ...
written 6 months ago by ole.tange3.9k
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Answer: A: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
... **EXAMPLE: Call program with FASTA sequence** FASTA files have the format: ...
written 10 months ago by ole.tange3.9k
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Answer: A: Calculating Shannon entropy for RNA sequences in multi-fasta using rnaentropy
... With GNU Parallel (https://www.biostars.org/p/63816/) you would do: cat in.fasta | parallel --pipe -N1 --recstart '>' --rrs 'read a; echo Doing "$a"; ./RNAentropy -s $(tr -d "\n")' From [GNU Parallel Tutorial: Informational](https://www.gnu.org/software/parallel/parallel_tutoria ...
written 10 months ago by ole.tange3.9k • updated 10 months ago by zx87549.6k
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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 13 months ago by ole.tange3.9k
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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 13 months ago by ole.tange3.9k
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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 18 months ago by ole.tange3.9k

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Popular Question 29 days ago, created a question with more than 1,000 views. For Got Multiple Cpus? Activate Them With Gnu Parallel
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Job Manager to parallelize otherwise consecutive bash scripts..?
Scholar 6 weeks ago, created an answer that has been accepted. For A: Job Manager to parallelize otherwise consecutive bash scripts..?
Great Question 6 weeks ago, created a question with more than 5,000 views. For Got Multiple Cpus? Activate Them With Gnu Parallel
Scholar 9 weeks ago, created an answer that has been accepted. For A: Job Manager to parallelize otherwise consecutive bash scripts..?
Great Question 5 months ago, created a question with more than 5,000 views. For Got Multiple Cpus? Activate Them With Gnu Parallel
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Teacher 3.6 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 5.3 years ago, created a question with more than 1,000 views. For Got Multiple Cpus? Activate Them With Gnu Parallel

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