[med-svn] [phylophlan] 05/10: Go with local usearch5 package. As a consequence the phylophlan package can not be released since usearch5 is not distributable
Andreas Tille
tille at debian.org
Fri Dec 1 15:01:03 UTC 2017
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 <tille at 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 <tille at 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-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at 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 <tille at 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"
--
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