Whole-genome shotgun assembler from TIGR
Created attachment 116763 [details] tigr-assembler-2.0.ebuild The latest version will be available at http://overlays.gentoo.org/proj/sunrise/browser/sunrise/sci-biology/tigr-assembler
(In reply to comment #1) > Created an attachment (id=116763) [edit] > tigr-assembler-2.0.ebuild > > The latest version will be available at > > http://overlays.gentoo.org/proj/sunrise/browser/sunrise/sci-biology/tigr-assembler > Hi, I've been writing an ebuild for this too, and it is essentially the same. The only thing I would suggest is a different run_TA script made in bash instead of csh (that is somehow deprecated on gentoo). One can put this run_TA in FILESDIR and install it in place of the one in $WORKDIR/TIGR_Assembler_v2/bin
Created attachment 117410 [details] the bash alternative for run_TA
> Hi, I've been writing an ebuild for this too, and it is essentially the same. > The only thing I would suggest is a different run_TA script made in bash > instead of csh (that is somehow deprecated on gentoo). One can put this run_TA > in FILESDIR and install it in place of the one in > $WORKDIR/TIGR_Assembler_v2/bin Thanks for catching this, I should have put in a dependency on csh/tcsh at least. I'll add this to my ebuild.
Deprecated isn't quite the right way to put it, but it pulls in an additional dependency for what is often a trivial shell script. If it's easy to rewrite in portable sh or bash (which it seems to be here), do it. Otherwise, settle for csh.
The current ebuild still does not install the run_TA script for me on ~x86. Please fix and write some documenting usage lines into it, thanks.
A link to some more description and the original article where it was published: http://www.jcvi.org/cms/publications/listing/abstract/article/tigr-assembler-a-new-tool-for-assembling-large-shotgun-sequencing-projects/
In sci overlay now. Sunrise copy has been removed.
I committed the bourne-shell based run_TA into the science overlay, the old script is installed as /usr/bin/run_TA.csh but no app-shells/tcsh dependency, also added src_test(), commented out "^CC = cc" in the Makefile, added ~amd64.
