Author: tille Date: 2016-05-24 13:28:23 +0000 (Tue, 24 May 2016) New Revision: 22013
Added: trunk/packages/phylophlan/trunk/debian/README.test Modified: trunk/packages/phylophlan/trunk/debian/changelog trunk/packages/phylophlan/trunk/debian/patches/debian_tools.patch trunk/packages/phylophlan/trunk/debian/patches/series trunk/packages/phylophlan/trunk/debian/patches/use_vsearch.patch Log: Update TODO Added: trunk/packages/phylophlan/trunk/debian/README.test =================================================================== --- trunk/packages/phylophlan/trunk/debian/README.test (rev 0) +++ trunk/packages/phylophlan/trunk/debian/README.test 2016-05-24 13:28:23 UTC (rev 22013) @@ -0,0 +1,8 @@ + + + phylophlan -u example_corynebacteria --nproc 4 + + --> Requires usearch! + --> We need to install examples from input/ dir into examples package + and let the code point to the location + Modified: trunk/packages/phylophlan/trunk/debian/changelog =================================================================== --- trunk/packages/phylophlan/trunk/debian/changelog 2016-05-24 07:25:26 UTC (rev 22012) +++ trunk/packages/phylophlan/trunk/debian/changelog 2016-05-24 13:28:23 UTC (rev 22013) @@ -1,5 +1,9 @@ phylophlan (1.1.0-1) UNRELEASED; urgency=medium * Initial release (Closes: #<bug>) + TODO: + * Find a replacement for usearch that can deal with proteins as well + * install examples from input/ dir into examples package and let the + code point to the location (see debian/README.test how to test this) -- Andreas Tille <[email protected]> Mon, 23 May 2016 16:09:13 +0200 Modified: trunk/packages/phylophlan/trunk/debian/patches/debian_tools.patch =================================================================== --- trunk/packages/phylophlan/trunk/debian/patches/debian_tools.patch 2016-05-24 07:25:26 UTC (rev 22012) +++ trunk/packages/phylophlan/trunk/debian/patches/debian_tools.patch 2016-05-24 13:28:23 UTC (rev 22013) @@ -9,7 +9,7 @@ def dep_checks(): - for prog in ["FastTree", "usearch", "muscle", "tblastn"]: -+ for prog in ["fasttree", "vsearch", "muscle", "tblastn"]: ++ for prog in ["fasttree", "usearch", "muscle", "tblastn"]: try: with open(os.devnull, 'w') as devnull: sb.call([prog], stdout=devnull, stderr=devnull) Modified: trunk/packages/phylophlan/trunk/debian/patches/series =================================================================== --- trunk/packages/phylophlan/trunk/debian/patches/series 2016-05-24 07:25:26 UTC (rev 22012) +++ trunk/packages/phylophlan/trunk/debian/patches/series 2016-05-24 13:28:23 UTC (rev 22013) @@ -1,4 +1,4 @@ debian_tools.patch datadir.patch -use_vsearch.patch +# use_vsearch.patch --> see https://lists.debian.org/debian-med/2016/05/msg00091.html fasttree_name.patch Modified: trunk/packages/phylophlan/trunk/debian/patches/use_vsearch.patch =================================================================== --- trunk/packages/phylophlan/trunk/debian/patches/use_vsearch.patch 2016-05-24 07:25:26 UTC (rev 22012) +++ trunk/packages/phylophlan/trunk/debian/patches/use_vsearch.patch 2016-05-24 13:28:23 UTC (rev 22013) @@ -3,6 +3,10 @@ Description: Debian can not package usearch which is non-free but it has the free replacement vsearch which is currently under active development and performs better than usearch +Remark: According to + https://lists.debian.org/debian-med/2016/05/msg00091.html + in this case vsearch doese not serve as a replacement for usearch. + Thus for the moment the patch needs to be deactivated --- a/phylophlan.py +++ b/phylophlan.py _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
