kloetzl / biozsh Goto Github PK

A really cool package! Just set it up, used @iimog's fix (#2) to get the path right. And just in case it might be useful for others - my quick fix to install and load it as a oh-my-zsh plugin:

cd ~/.oh-my-zsh/custom/plugins/
git clone https://github.com/kloetzl/biozsh
cd biozsh
ln -s biozsh.sh biozsh.plugin.zsh # autoloads .plugin.zsh files

Add to ~/.zshrc plugin list.

plugins=(git ... biozsh)

Jellyfish comes with good documentation. Any user of biozsh with interest in jellyfish, this might be a valuable first issue to learn the basics of writing a completion function. Mark _jellyfish as executable, when done.

What is the best way to install zsh completions? Is there even a proper cross-platform way to find the fpath?

Also, how do I install wrappers‽

The bedtools are properly documented, however, I don't use them. Help by an interested person would be greatly appreciated. Mark the _bedtools file as executable, when done.

Hi there,

This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's -max_target_seqs parameter:

• completions/_blastp
• completions/_tblastx
• completions/_blastn
• completions/_tblastn

Based on the recently published report, Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows, there is a strong chance that this parameter is misused in your repository.

If the use of this parameter was intentional, please feel free to ignore and close this issue but I would highly recommend to add a comment to your source code to notify others about this use case. If this is a duplicate issue, please accept my apologies for the redundancy as this simple automation is not smart enough to identify such issues.

Thank you!
-- Arman (armish/blast-patrol)

Hey @kloetzl
thanks for this wonderful set of completions. Unfortunately they do not work out of the box with antigen.
I'm using zsh 5.1.1 (x86_64-ubuntu-linux-gnu) with Antigen v2.2.2 (bd9d533).

The simple command

antigen bundle kloetzl/biozsh

installs the repo just fine (to ~/.antigen/bundles/kloetzl/biozsh) and sources the included biozsh.zsh.
However the sourcing is done with the home folder as working directory so the $PWD inside biozsh.zsh does not work properly. Sourcing it manually from anywhere but the biozsh directory results in the same problem. A workaround is to determine the real location of the zsh file using this expression:

BIOZSH_DIR="${funcsourcetrace[1]%/*}"

This works according to this SO answer. This way the completions should work no matter from where the file is sourced. It also fixes the installation with antigen.

For tools like bedtools, there are too many subcommands and not everyone is implemented for completion. Also most of them are not frequently used and maybe change by time.

Can we have a minimal filename completes when a subcommand is not defined or newly added? Just like default behavior without completion script.

e.g. bedtools maskfasta and samtools fastq

Here is an assorted list of tools for which completions might be of interest to some users.

• annovar
• bamstats
• bcftools
• beagle
• BigWig
• bismark
• callisto
• chimira
• cufflinks
• cutadapt
• # DEseq2 - not a command line tool
• Diamond — Done by @cgjosephlee in #9
• edgeR
• elprep
• exomedepth
• impute
• kraken
• micca
• muscan
• nextgenmap
• Picard
• pindel
• qualimap
• quiime2
• sambamba
• scalpel
• sleuth
• snpeff
• star
• sylamer
• tandemrepeatsfinder
• tophat2
• trimgalore
• varscan2
• vntrseek
• zoom