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

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/

varnion commented on 2014-08-20 14:50 (UTC)

Biopieces tested: 85 Tests run: 292 OK: 280 FAIL: 9 WARNING: 3 Time: 22 secs Hooray! I installed all the necessary stuff, minus Ray, vmatch and mysql. There are still some issues, though. For instance, blast/usearch tests still fail, test_uniq_seq passes or fails at random... Regardless, these are the changes in order to make the package work: --- biopieces.sh: export BP_DIR="/opt/biopieces" # Directory where biopieces are installed export BP_DATA="$HOME/.biopieces/data" # Contains genomic data etc. export BP_TMP="/tmp/$USER/biopieces" # Required temporary directory. export BP_LOG="$BP_TMP/log" # Required log directory. --- PKGBUILD (starting on line 44): # source the constant for the test suite export BP_DIR="opt/$pkgname" export BP_TMP="tmp" export BP_LOG="$BP_TMP/log" source "$BP_DIR/bp_conf/bashrc" mkdir -p $BP_LOG # permission to write on bp_test chmod a+w "opt/$pkgname/bp_test" chmod a+w "opt/$pkgname/bp_test/in" chmod a+w "opt/$pkgname/bp_test/out" # calling test /bin/bash "opt/$pkgname/bp_test/test_all" # remove unnecessary files rm -R $BP_TMP # export the apropriate variables source etc/profile.d/$pkgname.sh --- PKGBUILD (dependencies): depends=('perl' 'ruby' 'perl-svg' 'perl-bit-vector' 'perl-term-readkey' 'perl-dbi' 'perl-xml-parser' 'perl-carp-clan' 'perl-class-inspector' 'perl-html-parser' 'perl-soap-lite' 'perl-uri' 'perl-inline' 'perl-parse-recdescent' 'perl-dbd-mysql' 'ruby-gnuplot' 'ruby-narray' 'perl-json-xs') makedepends=('svn') checkdepends=() optdepends=('blast: legacy blast' 'gnuplot' 'blat' 'bwa' 'bowtie' 'bowtie2' 'hmmer' 'mummer' 'muscle') --- ruby-rubyinline and ruby-terminal-table should also be included on dependencies, but there is no package for them... I'll try to create it. I'll also try to create packages for scan_for_matches, prodigal, idba-hybrid and velvet. usearch and vmatch require registration =/

varnion commented on 2014-08-19 04:11 (UTC)

u r welcome! (this is my first time actually contributing. I'm still trying to understand how these packages work...) There's one more perl dependency, not listed on biopieces page: perl-json-xs After installing all perl dependencies and all ruby gems from aur (ruby-gnuplot, ruby-narray) and with "gem install package" (terminal-table, RubyInline), I got this: Biopieces tested: 85 Tests run: 292 OK: 241 FAIL: 33 WARNING: 18 Time: 125 secs I also needed to change permissions on /opt/biopieces/bp_test (the test program writes stuff there...)

confusedfla commented on 2014-08-18 09:57 (UTC)

thanks a lot for listing all the required perl modules - I added them and removed the dependency to perl-module-build-tiny or perl-version. However the unit tests still fail at the same rate. If you have time and want to have a deeper look at the unit tests, feel welcome ;-) Biopieces tested: 85 Tests run: 292 OK: 181 FAIL: 95 WARNING: 16 Time: 36 secs (Also if you want to be the maintainer of this package, just let me know.)

varnion commented on 2014-08-16 21:50 (UTC)

biopieces dont actually need perl-module-build-tiny or perl-version. both are included on perl 5.20.0-5: perl-module-build perl-time-hires perl-version perl-db_file and, except for perl-lwp, all other modules can be found on official repos or aur: extra/perl-bit-vector 7.3-2 extra/perl-term-readkey 2.32-1 extra/perl-dbi 1.631-2 extra/perl-xml-parser 2.41-5 extra/perl-carp-clan 6.04-3 extra/perl-class-inspector 1.28-2 extra/perl-html-parser 3.71-3 extra/perl-soap-lite 1.11-1 extra/perl-uri 1.64-1 community/perl-inline 0.55-1 community/perl-parse-recdescent 1.967009-2 extra/perl-dbd-mysql 4.027-2 aur/perl-svg 2.59-1 a lot of perl-lwp "subpackages" exists on official repositories and aur. i'm not sure which one to use...

confusedfla commented on 2014-04-26 06:02 (UTC)

a lot of the required perl and ruby modules are still missing. Anyway basic functionality is given (62%). Biopieces tested: 85 Tests run: 292 OK: 183 FAIL: 93 WARNING: 16 Time: 45 secs See this link for the whole dependency list https://code.google.com/p/biopieces/wiki/Installation