taskSavannah Administration - Tasks: task #13105, Submission of Bioinformatics...


task #13105: Submission of Bioinformatics Source Release Collection

Submitted by:  Brandon Invergo <brandon>
Submitted on:  Mon 24 Feb 2014 08:46:28 PM UTC  
Should Start On: Sun 23 Feb 2014 11:00:00 PM UTCShould be Finished on: Wed 05 Mar 2014 11:00:00 PM UTC
Category: Project ApprovalPriority: 5 - Normal
Status: CancelledPrivacy: Public
Percent Complete: 0%Assigned to: Joan Lledó <jllledo>
Open/Closed: ClosedEffort: 0.00

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Mon 03 Mar 2014 11:50:42 PM UTC, comment #1:

I've decided to self-host this project, so we can go ahead and cancel this request. Sorry for the noise!

Brandon Invergo <brandon>
Site Administrator
Mon 24 Feb 2014 08:46:28 PM UTC, original submission:

A new project has been registered at Savannah
This project account will remain inactive until a site admin approves or discards the registration.

Registration Administration

While this item will be useful to track the registration process, approving or discarding the registration must be done using the specific Group Administration page, accessible only to site administrators, effectively logged as site administrators (superuser):

Registration Details

  • Name: Bioinformatics Source Release Collection
  • System Name: biosrc
  • Type: non-GNU software and documentation
  • License: GNU General Public License v3 or later (Files derived from GSRC as well as new BioSRC files (i.e. the Makefiles containing package build recipies) are under the GPLv3 or later. Files originating from GAR and GARstow are under the All Permissive license.

All software installable via BioSRC is available under free software licenses; each package's license is noted in its Makefile and is printed when the user requests package information (make pkg-info).

Documentation is under the GFDL 1.2 or later.)


BioSRC (based on GNU SRC) is a Ports-like system for easily installing bioinformatics software. There are several reasons why this software is needed. First, most GNU/Linux distributions do not include a wide range of modern bioinformatics software packages, so packages sources need to be searched for and installed the old-fashioned way. Second, most researchers use shared computing resources (clusters) and do not have administrator rights for installing new software. Thus, they either request that software be installed for them or they must install it themselves to a directory under their control. To this end, BioSRC greatly simplifies the process of fetching and installing the software, particularly since bioinformatics software tends to exhibit apalling packaging standards, often requiring manual intervention.

Other Software Required:

GNU Make - GPLv3orlater - http://www.gnu.org/s/make
GNU sed - GPLv3orlater - http://www.gnu.org/s/sed
GNU wget - GPLv3orlater - http://www.gnu.org/s/wget
GNU coreutils - GPLv3orlater - http://www.gnu.org/s/coreutils

Other Comments:

Thanks for taking the time to review this!

Tarball URL:


Brandon Invergo <brandon>
Site Administrator


(Note: upload size limit is set to 16384 kB, after insertion of the required escape characters.)

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Depends on the following items: None found

Items that depend on this one: None found


Carbon-Copy List
  • -unavailable- added by jllledo (Updated the item)
  • -unavailable- added by brandon (Submitted the item)

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    Follow 3 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Tue 04 Mar 2014 06:29:52 PM UTCjllledoStatusNone=>Cancelled
      Assigned toNone=>jllledo

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