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AUR (en) - biopieces

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Package Details: biopieces r2311-1

Git Clone URL: https://aur-dev.archlinux.org/biopieces.git (read-only)
Package Base: biopieces
Description: Bioinformatic framework of tools easily used and easily created
Upstream URL: http://biopieces.googlecode.com/
Licenses: GPL2
Submitter: confusedfla
Maintainer: confusedfla
Last Packager: confusedfla
Votes: 2
Popularity: 0.000000
First Submitted: 2014-04-26 05:45
Last Updated: 2015-06-16 19:29

Dependencies (34)

Required by (0)

Sources (3)

Latest Comments

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khughitt commented on 2016-11-18 17:39

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

confusedfla commented on 2014-11-26 00:16

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

> 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

varnion commented on 2014-08-27 15:01

> 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 are mailed for u. At least for usearch u just need to make the binary executable, rename to uclust and move/symlink to /usr/bin.

confusedfla commented on 2014-08-24 13:45

> 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

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

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

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

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

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...)