This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository phylophlan.
commit e784d9afe7f3fc650d0a34a90f1c7ee65b033ddf Author: Andreas Tille <ti...@debian.org> Date: Mon Jul 11 16:04:53 2016 +0000 Go with local usearch5 package. As a consequence the phylophlan package can not be released since usearch5 is not distributable --- debian/README.source | 10 ++++ debian/control | 4 +- debian/patches/debian_tools.patch | 2 +- debian/patches/series | 2 +- debian/patches/use_vsearch.patch | 87 ++++---------------------------- debian/phylophlan-examples.install | 1 + debian/{install => phylophlan.install} | 0 debian/{manpages => phylophlan.manpages} | 0 debian/postinst | 2 +- 9 files changed, 25 insertions(+), 83 deletions(-) diff --git a/debian/README.source b/debian/README.source new file mode 100644 index 0000000..a99936e --- /dev/null +++ b/debian/README.source @@ -0,0 +1,10 @@ +According to + + https://lists.debian.org/debian-med/2016/05/msg00091.html + +phylophlan needs usearch which is non-free and non-distributable. + +You need to build your local usearch5 package (phylophlan needs +version 5 of usearch) if you want to use this package. + + -- Andreas Tille <ti...@debian.org> Mon, 11 Jul 2016 16:17:01 +0200 diff --git a/debian/control b/debian/control index 6bf2529..3475709 100644 --- a/debian/control +++ b/debian/control @@ -1,7 +1,7 @@ Source: phylophlan Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Uploaders: Andreas Tille <ti...@debian.org> -Section: science +Section: contrib/science Priority: optional Build-Depends: debhelper (>= 9), python-all, @@ -16,7 +16,7 @@ Architecture: all Depends: ${python:Depends}, ${misc:Depends}, fasttree, - vsearch, + usearch5, muscle, ncbi-blast+, python-biopython diff --git a/debian/patches/debian_tools.patch b/debian/patches/debian_tools.patch index aa1afce..470490f 100644 --- a/debian/patches/debian_tools.patch +++ b/debian/patches/debian_tools.patch @@ -9,7 +9,7 @@ Description: Use Debian packaged tools with correct names def dep_checks(): - for prog in ["FastTree", "usearch", "muscle", "tblastn"]: -+ for prog in ["fasttree", "usearch", "muscle", "tblastn"]: ++ for prog in ["fasttree", "usearch5", "muscle", "tblastn"]: try: with open(os.devnull, 'w') as devnull: sb.call([prog], stdout=devnull, stderr=devnull) diff --git a/debian/patches/series b/debian/patches/series index 0d35121..12c55fa 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,4 +1,4 @@ debian_tools.patch datadir.patch -# use_vsearch.patch --> see https://lists.debian.org/debian-med/2016/05/msg00091.html +use_vsearch.patch fasttree_name.patch diff --git a/debian/patches/use_vsearch.patch b/debian/patches/use_vsearch.patch index 57a8740..c566363 100644 --- a/debian/patches/use_vsearch.patch +++ b/debian/patches/use_vsearch.patch @@ -1,96 +1,27 @@ Author: Andreas Tille <ti...@debian.org> Last-Update: Mon, 23 May 2016 16:09:13 +0200 -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 +Description: According to upstream we need to use userach5 which + is non-distributable 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 -@@ -153,8 +153,9 @@ def init(): - info("Done!\n") +@@ -154,7 +154,8 @@ def init(): if not os.path.exists( ppa_wdb ): -- info("Generating "+ppa_wdb+" (usearch indexed DB)... ") + info("Generating "+ppa_wdb+" (usearch indexed DB)... ") - sb.call( ["usearch","-quiet", -+ info("Generating "+ppa_wdb+" (vsearch indexed DB)... ") -+ print("vsearch -quiet --makewdb %s --output %s" % (ppa_fna,ppa_wdb)) -+ sb.call( ["vsearch","-quiet", ++ print("usearch5 -quiet --makewdb %s --output %s" % (ppa_fna,ppa_wdb)) ++ sb.call( ["usearch5","-quiet", "--makewdb",ppa_fna, "--output",ppa_wdb]) info("Done!\n") -@@ -265,29 +266,29 @@ def exe_usearch(x): - screen_usearch_wdb( x[5] ) - info( x[5] + " generated!\n" ) - except OSError: -- error( "OSError: fatal error running usearch." ) -+ error( "OSError: fatal error running vsearch." ) - return - except ValueError: -- error( "ValueError: fatal error running usearch." ) -+ error( "ValueError: fatal error running vsearch." ) - return - except KeyboardInterrupt: -- error( "KeyboardInterrupt: usearch process interrupted." ) -+ error( "KeyboardInterrupt: vsearch process interrupted." ) - return - - - def faa2ppafaa( inps, nproc, proj ): - inp_fol = "input/"+proj+"/" -- dat_fol = "data/"+proj+"/usearch/" -+ dat_fol = "data/"+proj+"/vsearch/" - pool = mp.Pool( nproc ) - mmap = [(inp_fol+i+'.faa', dat_fol+i+'.b6o') for i in inps if not os.path.exists(dat_fol+i+'.b6o')] - - if not os.path.isdir(dat_fol): os.mkdir(dat_fol) # create the tmp directory if does not exists - - if not mmap: -- info("All usearch runs already performed!\n") -+ info("All vsearch runs already performed!\n") +@@ -287,7 +288,7 @@ def faa2ppafaa( inps, nproc, proj ): + info("All usearch runs already performed!\n") else: info("Looking for PhyloPhlAn proteins in input faa files\n") - us_cmd = [ ["usearch","-quiet", -+ us_cmd = [ ["vsearch","-quiet", ++ us_cmd = [ ["usearch5","-quiet", "-wdb",ppa_wdb, "-blast6out",o, "-query",i, -@@ -295,7 +296,7 @@ def faa2ppafaa( inps, nproc, proj ): - pool.map_async( exe_usearch, us_cmd ) - pool.close() - pool.join() -- info("All usearch runs performed!\n") -+ info("All vsearch runs performed!\n") - - if os.path.exists(dat_fol+up2prots): - return -@@ -418,7 +419,7 @@ def blast(inps, nproc, proj, blast_full= - - def gens2prots(inps, proj ): - inp_fol = "input/"+proj+"/" -- dat_fol = "data/"+proj+"/usearch/" -+ dat_fol = "data/"+proj+"/vsearch/" - - if not os.path.isdir(dat_fol): os.mkdir(dat_fol) # create the tmp directory if does not exists - -@@ -523,7 +524,7 @@ def exe_muscle(x): - error( "ValueError: fatal error running muscle." ) - raise e - except KeyboardInterrupt, e: -- error( "KeyboardInterrupt: usearch process muscle." ) -+ error( "KeyboardInterrupt: vsearch process muscle." ) - raise e - except Exception, e: - error( e ) -@@ -881,7 +882,7 @@ def tax_curation_test( proj, tax, - - def merge_usearch_blast(inps, proj): - dat_fol = 'data/'+proj+'/' -- usearch_fol = 'data/'+proj+'/usearch/' -+ usearch_fol = 'data/'+proj+'/vsearch/' - tblastn_fol = 'data/'+proj+'/tblastn/' - usearch_files = [] - tblastn_files = [] diff --git a/debian/phylophlan-examples.install b/debian/phylophlan-examples.install new file mode 100644 index 0000000..1226998 --- /dev/null +++ b/debian/phylophlan-examples.install @@ -0,0 +1 @@ +input/example_* usr/share/doc/phylophlan/examples diff --git a/debian/install b/debian/phylophlan.install similarity index 100% rename from debian/install rename to debian/phylophlan.install diff --git a/debian/manpages b/debian/phylophlan.manpages similarity index 100% rename from debian/manpages rename to debian/phylophlan.manpages diff --git a/debian/postinst b/debian/postinst index 54cadfc..037cc45 100755 --- a/debian/postinst +++ b/debian/postinst @@ -3,7 +3,7 @@ case "$1" in configure) # enable users to unpack data files - find /var/lib/phylophlan -type d -exec chmod a+w \{\} \; + find /var/lib/phylophlan -type d -exec chmod 1777 \{\} \; ;; abort-upgrade|abort-remove|abort-deconfigure) echo "$1" -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/phylophlan.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit