Package Details: biopieces 2.0-1

Git Clone URL: https://aur.archlinux.org/biopieces.git (read-only, click to copy)
Package Base: biopieces
Description: Bioinformatic framework of tools easily used and easily created
Upstream URL: http://maasha.github.io/biopieces/
Licenses: GPL2
Submitter: confusedfla
Maintainer: None
Last Packager: clintval
Votes: 2
Popularity: 0.000000
First Submitted: 2014-04-26 05:45 (UTC)
Last Updated: 2018-03-17 01:55 (UTC)

Latest Comments

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clintval commented on 2018-03-17 01:55 (UTC)

Does anyone use this? I don't but volunteered to maintain....

confusedfla commented on 2017-12-15 03:45 (UTC)

I don't use this anymore. Disowning.

khughitt commented on 2016-11-18 17:39 (UTC)

SVN repo no longer being used; now hosted at https://github.com/maasha/biopieces

confusedfla commented on 2014-11-26 00:16 (UTC)

I added ruby-terminal-table and ruby-rubyinline Biopieces tested: 85 Tests run: 292 OK: 243 FAIL: 32 WARNING: 17 Time: 55 secs UClust is freely available: http://www.drive5.com/uclust/downloads1_2_22q.html

varnion commented on 2014-08-27 16:38 (UTC)

> Testing auxiliary program - "blastall": WARNING > Testing auxiliary program - "formatdb": WARNING Just install legacy blast (https://aur.archlinux.org/packages/blast/) U can finally add ruby-terminal-table and ruby-rubyinline as deps. (https://aur.archlinux.org/packages/ruby-terminal-table/, https://aur.archlinux.org/packages/ruby-rubyinline/) I'm still working on the others but I can't help with usearch/uclust or vmatch. They require registration and their binaries sent to yr mail. At least for usearch u just need to make the binary executable, mv to /usr/bin/usearch

confusedfla commented on 2014-08-24 13:45 (UTC)

> there is something odd happening while running makepkg: almost all tests fail! I forgot to source the bp_conf/bashrc in the new check function. > I plan to create packages for those unavailable on AUR That would be totally awesome :-) Those programs are missing on my machine. Testing auxiliary program - "blastall": WARNING Testing auxiliary program - "formatdb": WARNING Testing auxiliary program - "idba_hybrid": WARNING Testing auxiliary program - "prodigal": WARNING Testing auxiliary program - "Ray": WARNING Testing auxiliary program - "scan_for_matches": WARNING Testing auxiliary program - "usearch": WARNING Testing auxiliary program - "velveth": WARNING Testing auxiliary program - "velvetg": WARNING Testing auxiliary program - "vmatch": WARNING

varnion commented on 2014-08-23 10:40 (UTC)

I tested the new PKGBUILD. great work! there is something odd happening while running makepkg: almost all tests fail! Biopieces tested: 85 Tests run: 292 OK: 27 FAIL: 262 WARNING: 3 Time: 1 secs but after installing the new package generated everything goes as expected, so no problem: Biopieces tested: 85 Tests run: 292 OK: 280 FAIL: 9 WARNING: 3 Time: 22 secs It came to my attention now that some biopieces rely on python2, but arch uses python3 by default. therefore, we must change the shebang lines accordingly (#!/usr/bin/python to #!/usr/bin/python2) adding this to the check function should do the trick: # patch python2 scripts find 'code_python' -type f -exec sed -i 's/#!\/usr\/bin\/python/&2/' {} \; also, python2 should be added as dependency (or would it be optional dep?)

varnion commented on 2014-08-23 10:28 (UTC)

U need to install the optional deps (some biopieces rely on them). On my notebook, I only on the required deps: Biopieces tested: 85 Tests run: 292 OK: 241 FAIL: 33 WARNING: 18 Time: 125 secs In my desk I have all deps (including some not available on AUR): Biopieces tested: 85 Tests run: 292 OK: 280 FAIL: 9 WARNING: 3 Time: 22 secs Testing auxiliary program - "blastall": OK Testing auxiliary program - "blat": OK Testing auxiliary program - "bwa": OK Testing auxiliary program - "bowtie": OK Testing auxiliary program - "bowtie2": OK Testing auxiliary program - "formatdb": OK Testing auxiliary program - "hmmsearch": OK Testing auxiliary program - "gnuplot": OK Testing auxiliary program - "idba_hybrid": OK Testing auxiliary program - "muscle": OK Testing auxiliary program - "mummer": OK Testing auxiliary program - "mysql": WARNING Testing auxiliary program - "prodigal": OK Testing auxiliary program - "Ray": WARNING Testing auxiliary program - "scan_for_matches": OK Testing auxiliary program - "usearch": OK Testing auxiliary program - "velveth": OK Testing auxiliary program - "velvetg": OK Testing auxiliary program - "vmatch": WARNING I plan to create packages for those unavailable on AUR (except usearch/uclust and vmatch, which require registration). the AUR package 'rubyinline' dont work at all and also should be named 'ruby-rubyinline' (according to https://wiki.archlinux.org/index.php/Ruby_Gem_Package_Guidelines)

confusedfla commented on 2014-08-23 02:45 (UTC)

thank you so much for your contribution. I updated the PKGBUILD according to your changes. There is a AUR package 'rubyinline' [1], but it is from 2010 and outdated (gem server down). Biopieces tested: 85 Tests run: 292 OK: 249 FAIL: 33 WARNING: 10 Time: 39 secs What did you do to get down to only 9 failing tests? [1] https://aur.archlinux.org/packages/rubyinline/

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