User: SaltedPork

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SaltedPork60
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Posts by SaltedPork

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Comment: C: I'm putting a pipeline into docker, where do I store the tar files for my depend
... Yep, it sure does help, thanks. ...
written 7 days ago by SaltedPork60
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Comment: C: I'm putting a pipeline into docker, where do I store the tar files for my depend
... What about for programs that can't be downloaded using conda, or apt-get and their only source is a tarball, where do you keep those? ...
written 7 days ago by SaltedPork60
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I'm putting a pipeline into docker, where do I store the tar files for my dependencies, on GitHub or within the Docker image?
... Lets say my pipeline requires me to install Samtools from the tar file. Would it make more sense to keep this tar file within the docker image in a folder, or should I put it on GitHub and have it be downloaded when using a command like ? RUN git clone www.linktogithub.com ...
pipeline docker written 7 days ago by SaltedPork60 • updated 7 days ago by Eric Lim370
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Comment: C: How to split fasta by '>' into a file each containing one sequence, and have the
... Hi, yes I did make a more suitable directory! Just didn't include it because the name is sensitive. I meant just looking at the loop, It's so simple but It just doesn't work. ...
written 16 days ago by SaltedPork60
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Comment: C: How to split fasta by '>' into a file each containing one sequence, and have the
... Thanks, this is good. I want to use this in combination with a find command, could you tell me why this isn't working? for files in `find . -type f -name '*.consensus.fasta' -not -path "*/temp/*"` do faSplit byname $files outRoot done ...
written 16 days ago by SaltedPork60
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How to split fasta by '>' into a file each containing one sequence, and have the name of that file be the ID?
... So far I have this awk '/^>/{s=++d".fasta"} {print > s}' file.fasta This splits the file just as I want it, but it produces new files called 1.fasta, 2.fasta, 3.fasta and so on. Is there a method of splitting it that has the new file name as the ID of the sequence inside? Or failing th ...
fasta split bash written 17 days ago by SaltedPork60 • updated 17 days ago by Pierre Lindenbaum103k
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Comment: C: How can I run lastz on multiple files using a bash loop and an associative array
... Wow, this is precisely what I want, and yes moving the files to same directory is a lot easier. Thankyou so much! ...
written 17 days ago by SaltedPork60
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How can I run lastz on multiple files using a bash loop and an associative array?
... The lastz command will look like: lastz reference.fasta sample.fasta --ambiguous=IUPAC --format=GENERAL > output.fasta I need to run lastz once for every sample file, because each sample file has to be compared to its own individual reference (I have one reference for each sample). I'm usi ...
find loop for bash written 18 days ago by SaltedPork60 • updated 17 days ago by cpad01124.1k
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Comment: C: How can I split a fasta file into many files, one file for each ID line and its
... Thanks, this is good enough! ...
written 4 weeks ago by SaltedPork60
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How can I split a fasta file into many files, one file for each ID line and its sequence
... I have a multiple fasta file, say with 7 sequences in it. I don't need to filter the ID line by anything, just want to separate it into 7 small fasta files. ...
fasta split written 4 weeks ago by SaltedPork60 • updated 4 weeks ago by genomax40k

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Supporter 5 weeks ago, voted at least 25 times.
Popular Question 13 months ago, created a question with more than 1,000 views. For Using BWA Index and i get 5 output files, but BWA-mem asks for just 1

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