Skip to content

274 contrib dependencies for life science applications: biodeps#309

Merged
boegel merged 15 commits intoeasybuilders:developfrom
fgeorgatos:274_contrib_biodeps
Jul 3, 2013
Merged

274 contrib dependencies for life science applications: biodeps#309
boegel merged 15 commits intoeasybuilders:developfrom
fgeorgatos:274_contrib_biodeps

Conversation

@fgeorgatos
Copy link
Copy Markdown
Contributor

This PR does a number of things:

  1. introduces biodeps (common life science applications dependencies) for goolf/1.4.10 (gnu) & ictce/5.3.0 (intel)
  2. adds a Boost version fixes a download bug for it identified in boost/zlib problems #304
  3. Provides an example with Mothur, whereby deps are collapsed within biodeps (-bare style)
  4. Provides an example with TopHat, to demo how Boost/SAMtools compatibility is handled (biodeps-extended)
  5. Add Perl-5.16.3-ictce-5.3.0* easyconfigs needed for certain bio* apps

Signed-off-by: Fotis Georgatos <[email protected]>
Signed-off-by: Fotis Georgatos <[email protected]>
Signed-off-by: Fotis Georgatos <[email protected]>
Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Why dance around the templating provided by EasyBuild like this?
There are two better alternatives for this:

  • use the namelower template, i.e.:
source_urls = [('http://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s', 'download')]
  • use the SOURCEFORGE_SOURCE constant:
source_urls = [SOURCEFORGE_SOURCE]

Please use the latter, which is equivalent to http://download.sourceforge.net/%(namelower)s (see eb --avail-easyconfig-templates), in all Boost easyconfigs. I have a branch ready that does just that, let me know if you'll clean this up or I should open the PR (which will cause conflicts with what you currently have).

Copy link
Copy Markdown
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

sorry for the delay, I fixed it as per 2nd suggestion; I'm fun of the motto:
less chars to type => less human in the process => more robust

Signed-off-by: Fotis Georgatos <[email protected]>
Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Please use SOURCEFORGE_SOURCE here too, and in all other Boost easyconfigs.

Copy link
Copy Markdown
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

OK, done... please review

boegel added a commit to boegel/easybuild-easyconfigs that referenced this pull request Jul 3, 2013
Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Use a different construction here, to avoid unintentionally breaking the match with versionsuffix and dep:

name = 'Mothur'
version = '1.30.2'

biodeps = 'biodeps'
biodeps_ver = '1.6'
versionsuffix = '-%s-%s' % (biodeps, biodeps_ver)

dependencies = [
    (biodeps, biodeps_ver),
    ('gzip', '1.5'),
]

Likewise for the other easyconfigs that use biodeps, of course.

@fgeorgatos
Copy link
Copy Markdown
Contributor Author

OK, pushed a new patchset (tested it, seems to work for the biodeps business fine and has examples for both cases)

fgeorgatos added a commit to fgeorgatos/easybuild-easyconfigs that referenced this pull request Jul 3, 2013
@fgeorgatos
Copy link
Copy Markdown
Contributor Author

merged in Ken's diffs; thanks for the contrib!

Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Homepage doesn't make sense... Better use (none), like we do for e.g. goolf.
Or maybe better, refer to the relevant HPCBIOS page?

Copy link
Copy Markdown
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

OK, good catch, thanks for spotting... fixed, please re-re-re-re-review!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants