I have no clue what this program does. I was asked to install it on our cluster so I went ahead and made an ebuild for it. This package has a fetch restriction. (From the web page) phrap is a program for assembling shotgun DNA sequence data. Among other features, it allows use of the entire read and not just the trimmed high quality part, it uses a combination of user-supplied and internally computed data quality information to improve assembly accuracy in the presence of repeats, it constructs the contig sequence as a mosaic of the highest quality read segments rather than a consensus, it provides extensive assembly information to assist in trouble-shooting assembly problems, and it handles large datasets. See the phrap/cross_match/swat documentation and phrap documentation for additional information.
Created attachment 73872 [details] the ebuild.
Created attachment 116856 [details] phrap-0.990329.ebuild The latest version will be available at http://overlays.gentoo.org/proj/sunrise/browser/sunrise/sci-biology/phrap
Andrey: Same here (see my comment in bug #114096). Looks like you will have fun adding licenses for these packages. They are mostly as-is with small, but essential (copyright concerning) additions, so, unfortunately, looks like we will need individual licenses here (added under licenses/ as usual).. George
Now available in the science overlay.
Andrey, the ebuild should in addition to emake run also: iv. If you have datasets with more than 64,000 reads, or that include sequences longer than 64,000 bp, you will need the .manyreads and/or .longreads versions of phrap and cross_match. These are created using the command # make manyreads And, the dobin line should in addition contain as well: "cross_match.manyreads phrap.longreads phrap.manyreads" Other than that looks fine.
Created attachment 175872 [details] improved phrap-0.990329.ebuild This ebuild installed for me: # equery files phrap [ Searching for packages matching phrap... ] * Contents of sci-biology/phrap-0.990329: /usr /usr/bin /usr/bin/cluster /usr/bin/cross_match /usr/bin/cross_match.manyreads /usr/bin/loco /usr/bin/phrap /usr/bin/phrap.longreads /usr/bin/phrap.manyreads /usr/bin/phrapview /usr/bin/swat /usr/share /usr/share/doc /usr/share/doc/phrap-0.990329 /usr/share/doc/phrap-0.990329/general.doc.txt.bz2 /usr/share/doc/phrap-0.990329/phrap.doc.txt.bz2 /usr/share/doc/phrap-0.990329/swat.doc.txt.bz2 #
Version 1.080812 is in CVS. Martin - Thanks for your contribution. The latest Phrap version incorporates the .longreads versions into the main file. Please help me test this package.
Andrey, but please push into cvs also the fixed ebuild for phrap-0.990329.ebuild which is the stable version of the package (what its developer Phil Green says). And mark that ebuild stable for x86 and amd64. Works fine for me. ;) The 1.080812 phrap version works for me fine as well although needs more memory. ;-)
BTW, why do I still have /usr/local/portage/layman/sunrise/sci-biology/phrap even after "layman -S"?
phrap-0.990329.ebuild should be made stable only for x86. amd64 must use the current beta version. The old version is know to be buggy on amd64.
In tree, so resolving FIXED.
