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tille pushed a commit to branch master
in repository phylophlan.
commit 03288cae443bc8f259445142983cb9966d4c475e
Author: Andreas Tille <ti...@debian.org>
Date: Mon May 23 16:02:05 2016 +0000
Inject first try to package phylophlan
---
debian/bin/phylophlan | 4 ++
debian/changelog | 5 +++
debian/clean | 1 +
debian/compat | 1 +
debian/control | 66 +++++++++++++++++++++++++++
debian/copyright | 31 +++++++++++++
debian/install | 4 ++
debian/manpages | 1 +
debian/patches/datadir.patch | 33 ++++++++++++++
debian/patches/debian_tools.patch | 15 +++++++
debian/patches/fasttree_name.patch | 17 +++++++
debian/patches/series | 4 ++
debian/patches/use_vsearch.patch | 92 ++++++++++++++++++++++++++++++++++++++
debian/phylophlan.1 | 65 +++++++++++++++++++++++++++
debian/postinst | 19 ++++++++
debian/postrm | 19 ++++++++
debian/rules | 9 ++++
debian/source/format | 1 +
debian/upstream/metadata | 11 +++++
debian/watch | 3 ++
20 files changed, 401 insertions(+)
diff --git a/debian/bin/phylophlan b/debian/bin/phylophlan
new file mode 100755
index 0000000..c5cf2fa
--- /dev/null
+++ b/debian/bin/phylophlan
@@ -0,0 +1,4 @@
+#!/bin/bash
+EXE=`basename $0`
+export PYTHONPATH="${PYTHONPATH:+$PYTHONPATH:}/usr/share/${EXE}/taxcuration"
+python /usr/share/${EXE}/${EXE}.py $@
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..89c718a
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+phylophlan (1.1.0-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <ti...@debian.org> Mon, 23 May 2016 16:09:13 +0200
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..c17e466
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1 @@
+taxcuration/*.pyc
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..6bf2529
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,66 @@
+Source: phylophlan
+Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
+Uploaders: Andreas Tille <ti...@debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ python-all,
+ dh-python
+Standards-Version: 3.9.8
+Vcs-Browser:
https://anonscm.debian.org/viewvc/debian-med/trunk/packages/phylophlan/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/phylophlan/trunk/
+Homepage: https://bitbucket.org/nsegata/phylophlan/wiki/Home
+
+Package: phylophlan
+Architecture: all
+Depends: ${python:Depends},
+ ${misc:Depends},
+ fasttree,
+ vsearch,
+ muscle,
+ ncbi-blast+,
+ python-biopython
+Description: microbial Tree of Life using 400 universal proteins
+ PhyloPhlAn is a computational pipeline for reconstructing highly
+ accurate and resolved phylogenetic trees based on whole-genome sequence
+ information. The pipeline is scalable to thousands of genomes and uses
+ the most conserved 400 proteins for extracting the phylogenetic signal.
+ PhyloPhlAn also implements taxonomic curation, estimation, and insertion
+ operations.
+ .
+ The main features of PhyloPhlAn are:
+ * completely automatic, as the user needs only to provide the
+ (unannotated) protein sequences of the input genomes (as multifasta
+ files of peptides - not nucleotides)
+ * very high topological accuracy and resolution because of the use of
+ up to 400 previously identified most conserved proteins
+ * the possibility of integrating new genomes in the already
+ reconstructed most comprehensive tree of life (3,171 microbial
+ genomes)
+ * taxonomy estimation for the newly inserted genomes
+ * taxonomic curation for the produced phylogenetic trees
+
+Package: phylophlan-examples
+Architecture: all
+Depends: ${misc:Depends},
+Description: microbial Tree of Life using 400 universal proteins (example data)
+ PhyloPhlAn is a computational pipeline for reconstructing highly
+ accurate and resolved phylogenetic trees based on whole-genome sequence
+ information. The pipeline is scalable to thousands of genomes and uses
+ the most conserved 400 proteins for extracting the phylogenetic signal.
+ PhyloPhlAn also implements taxonomic curation, estimation, and insertion
+ operations.
+ .
+ The main features of PhyloPhlAn are:
+ * completely automatic, as the user needs only to provide the
+ (unannotated) protein sequences of the input genomes (as multifasta
+ files of peptides - not nucleotides)
+ * very high topological accuracy and resolution because of the use of
+ up to 400 previously identified most conserved proteins
+ * the possibility of integrating new genomes in the already
+ reconstructed most comprehensive tree of life (3,171 microbial
+ genomes)
+ * taxonomy estimation for the newly inserted genomes
+ * taxonomic curation for the produced phylogenetic trees
+ .
+ This package contains some example data.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..27e2f39
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,31 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: PhyloPhlAn
+Source: https://bitbucket.org/nsegata/phylophlan/downloads
+
+Files: *
+Copyright: 2012-206 Nicola Segata and Curtis Huttenhower
+License: expat
+
+Files: debian/*
+Copyright: © 2016 maintainername <maintai...@e.mail>
+License: expat
+
+License: expat
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EV ENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR TH E USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..685fad2
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,4 @@
+phylophlan.py usr/share/phylophlan
+taxcuration usr/share/phylophlan
+data var/lib/phylophlan
+debian/bin usr
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/patches/datadir.patch b/debian/patches/datadir.patch
new file mode 100644
index 0000000..c4e0e62
--- /dev/null
+++ b/debian/patches/datadir.patch
@@ -0,0 +1,33 @@
+Author: Andreas Tille <ti...@debian.org>
+Last-Update: Mon, 23 May 2016 16:09:13 +0200
+Description: Move data to user writable dir
+
+--- a/phylophlan.py
++++ b/phylophlan.py
+@@ -31,16 +31,16 @@ import time
+
+
+ download = ""
+-ppa_fna = "data/ppa.seeds.faa"
+-ppa_fna_40 = "data/ppa.seeds.40.faa"
+-ppa_aln = "data/ppafull.aln.faa"
+-ppa_up2prots = "data/ppafull.up2prots.txt"
+-ppa_ors2prots = "data/ppafull.orgs2prots.txt"
+-ppa_tax = "data/ppafull.tax.txt"
+-ppa_alns = ("data/ppaalns/list.txt","data/ppaalns/ppa.aln.tar.bz2")
+-ppa_alns_fol = "data/ppaalns/"
+-ppa_xml = "data/ppafull.xml"
+-ppa_wdb = "data/ppa.wdb"
++ppa_fna = "/var/lib/phylophlan/data/ppa.seeds.faa"
++ppa_fna_40 = "/var/lib/phylophlan/data/ppa.seeds.40.faa"
++ppa_aln = "/var/lib/phylophlan/data/ppafull.aln.faa"
++ppa_up2prots = "/var/lib/phylophlan/data/ppafull.up2prots.txt"
++ppa_ors2prots = "/var/lib/phylophlan/data/ppafull.orgs2prots.txt"
++ppa_tax = "/var/lib/phylophlan/data/ppafull.tax.txt"
++ppa_alns =
("/var/lib/phylophlan/data/ppaalns/list.txt","/var/lib/phylophlan/data/ppaalns/ppa.aln.tar.bz2")
++ppa_alns_fol = "/var/lib/phylophlan/data/ppaalns/"
++ppa_xml = "/var/lib/phylophlan/data/ppafull.xml"
++ppa_wdb = "/var/lib/phylophlan/data/ppa.wdb"
+ up2prots = "up2prots.txt"
+ ors2prots = "orgs2prots.txt"
+ aln_tot = "aln.fna"
diff --git a/debian/patches/debian_tools.patch
b/debian/patches/debian_tools.patch
new file mode 100644
index 0000000..1817a55
--- /dev/null
+++ b/debian/patches/debian_tools.patch
@@ -0,0 +1,15 @@
+Author: Andreas Tille <ti...@debian.org>
+Last-Update: Mon, 23 May 2016 16:09:13 +0200
+Description: Use Debian packaged tools with correct names
+
+--- a/phylophlan.py
++++ b/phylophlan.py
+@@ -66,7 +66,7 @@ def error(s):
+
+
+ def dep_checks():
+- for prog in ["FastTree", "usearch", "muscle", "tblastn"]:
++ for prog in ["fasttree", "vsearch", "muscle", "tblastn"]:
+ try:
+ with open(os.devnull, 'w') as devnull:
+ sb.call([prog], stdout=devnull, stderr=devnull)
diff --git a/debian/patches/fasttree_name.patch
b/debian/patches/fasttree_name.patch
new file mode 100644
index 0000000..09c5a7c
--- /dev/null
+++ b/debian/patches/fasttree_name.patch
@@ -0,0 +1,17 @@
+Author: Andreas Tille <ti...@debian.org>
+Last-Update: Mon, 23 May 2016 16:09:13 +0200
+Description: Debian's executable has lower case spelling
+
+--- a/phylophlan.py
++++ b/phylophlan.py
+@@ -671,8 +671,8 @@ def fasttree( proj, integrate ):
+ if os.path.exists( outt ):
+ info("Final tree already built ("+outt+")!\n")
+ return
+- info("Start building the tree with FastTree ... \n")
+- cmd = [ "FastTree", "-quiet",
++ info("Start building the tree with fasttree ... \n")
++ cmd = [ "fasttree", "-quiet",
+ #"-fastest","-noml"
+ #"-gamma",
+ "-bionj","-slownni",
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..12c55fa
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,4 @@
+debian_tools.patch
+datadir.patch
+use_vsearch.patch
+fasttree_name.patch
diff --git a/debian/patches/use_vsearch.patch b/debian/patches/use_vsearch.patch
new file mode 100644
index 0000000..447acd0
--- /dev/null
+++ b/debian/patches/use_vsearch.patch
@@ -0,0 +1,92 @@
+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
+
+--- a/phylophlan.py
++++ b/phylophlan.py
+@@ -153,8 +153,9 @@ def init():
+ info("Done!\n")
+
+ if not os.path.exists( ppa_wdb ):
+- 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",
+ "--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")
+ else:
+ info("Looking for PhyloPhlAn proteins in input faa files\n")
+- us_cmd = [ ["usearch","-quiet",
++ us_cmd = [ ["vsearch","-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.1 b/debian/phylophlan.1
new file mode 100644
index 0000000..7c0d551
--- /dev/null
+++ b/debian/phylophlan.1
@@ -0,0 +1,65 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH PHYLOPHLAN "1" "May 2016" "phylophlan 1.1.0" "User Commands"
+.SH NAME
+phylophlan \- computational pipeline for reconstructing highly accurate and
resolved phylogenetic trees
+.SH SYNOPSIS
+.B phylophlan
+[\-h] [\-i] [\-u] [\-t] [\-\-tax_test TAX_TEST] [\-c]
+[\-\-cleanall] [\-\-nproc N] [\-\-blast_full] [\-v]
+[PROJECT NAME]
+.SH DESCRIPTION
+PhyloPhlAn is a computational pipeline for reconstructing highly accurate and
resolved
+phylogenetic trees based on whole\-genome sequence information. The pipeline
is scalable
+to thousands of genomes and uses the most conserved 400 proteins for
extracting the
+phylogenetic signal.
+PhyloPhlAn also implements taxonomic curation, estimation, and insertion
operations.
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+PROJECT NAME
+The basename of the project corresponding to the name of the input data folder
inside
+input/. The input data consist of a collection of multifasta files (extension
.faa)
+containing the proteins in each genome.
+If the project already exists, the already executed steps are not re\-ran.
+The results will be stored in a folder with the project basename in output/
+Multiple project can be generated and they safetely coexists.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-i\fR, \fB\-\-integrate\fR
+Integrate user genomes into the PhyloPhlAn tree
+.TP
+\fB\-u\fR, \fB\-\-user_tree\fR
+Build a phylogenetic tree using user genomes only
+.TP
+\fB\-t\fR, \fB\-\-taxonomic_analysis\fR
+Check taxonomic inconsistencies and refine/correct taxonomic labels
+.TP
+\fB\-\-tax_test\fR TAX_TEST
+nerrors:type:taxl:tmin:tex:name (alpha version, experimental!)
+.TP
+\fB\-c\fR, \fB\-\-clean\fR
+Clean the final and partial data produced for the specified project.
+(use \fB\-\-cleanall\fR for removing general installation and database files)
+.TP
+\fB\-\-cleanall\fR
+Remove all instalation and database file leaving untouched the initial
compressed data
+that is automatically extracted and formatted at the first pipeline run.
+Projects are not remove (specify a project and use \fB\-c\fR for removing
projects).
+.TP
+\fB\-\-nproc\fR N
+The number of CPUs to use for parallelizing the blasting
+[default 1, i.e. no parallelism]
+.TP
+\fB\-\-blast_full\fR
+If specified, tells blast to use the full dataset of universal proteins
+[default False, i.e. the small dataset of universal proteins is used]
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+Prints the current PhyloPhlAn version and exit
+.SH AUTHOR
+Nicola Segata (nseg...@hsph.harvard.edu) and Curtis Huttenhower
(chutt...@hsph.harvard.edu)
+.P
+This manpage was written by Andreas Tille for the Debian distribution and can
be used for any other usage of the program.
diff --git a/debian/postinst b/debian/postinst
new file mode 100755
index 0000000..54cadfc
--- /dev/null
+++ b/debian/postinst
@@ -0,0 +1,19 @@
+#!/bin/sh -e
+
+case "$1" in
+ configure)
+ # enable users to unpack data files
+ find /var/lib/phylophlan -type d -exec chmod a+w \{\} \;
+ ;;
+ abort-upgrade|abort-remove|abort-deconfigure)
+ echo "$1"
+ ;;
+ *)
+ echo "postinst called with unknown argument \`\$1'" >&2
+ exit 0
+ ;;
+esac
+
+#DEBHELPER#
+
+exit 0
diff --git a/debian/postrm b/debian/postrm
new file mode 100755
index 0000000..16a023d
--- /dev/null
+++ b/debian/postrm
@@ -0,0 +1,19 @@
+#!/bin/sh -e
+
+case "$1" in
+ remove|purge)
+ # Remove postentially unpackaged data
+ rm -rf /var/lib/phylophlan
+ ;;
+ upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
+ echo $1
+ ;;
+ *)
+ echo "postrm called with unknown argument \`\$1'" >&2
+ exit 0
+ ;;
+esac
+
+#DEBHELPER#
+
+exit 0
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..8fdd6bc
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+
+%:
+ dh $@ --with python2
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..66ea9bb
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+ Author: Nicola Segata and Daniela Börnigen and Xochitl C. Morgan and Curtis
Huttenhower
+ Title: "PhyloPhlAn is a new method for improved phylogenetic and taxonomic
placement of microbes"
+ Journal: Nature Communications
+ Year: 2013
+ Volume: 4
+ Pages: 2304
+ DOI: 10.1038/ncomms3304
+ PMID: 23942190
+ URL: http://www.nature.com/ncomms/2013/130814/ncomms3304/full/ncomms3304.html
+ eprint:
http://www.nature.com/ncomms/2013/130814/ncomms3304/pdf/ncomms3304.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..2567a1a
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+https://bitbucket.org/nsegata/phylophlan/downloads .*/(\d\S*)\.tar\.gz
--
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/srv/git.debian.org/git/debian-med/phylophlan.git
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