[med-svn] [python-biomaj3] 02/07: Import Debian patch 3.0.20-1
Olivier Sallou
osallou at debian.org
Sat Jan 14 13:41:47 UTC 2017
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch master
in repository python-biomaj3.
commit 764c6b150f5e03ff8f7dcae6db4dfa45e828877f
Author: Olivier Sallou <osallou at debian.org>
Date: Sat Jan 14 09:30:04 2017 +0000
Import Debian patch 3.0.20-1
---
debian/README.source | 2 +
debian/alu.properties | 41 +++
debian/biomaj3-doc.dirs | 1 +
debian/biomaj3-doc.doc-base | 10 +
debian/changelog | 5 +
debian/compat | 1 +
debian/control | 75 +++++
debian/copyright | 687 ++++++++++++++++++++++++++++++++++++++++
debian/global.properties-py | 115 +++++++
debian/global.properties-py3 | 115 +++++++
debian/patches/series | 0
debian/python-biomaj3.dirs | 6 +
debian/python-biomaj3.examples | 1 +
debian/python3-biomaj3.dirs | 6 +
debian/python3-biomaj3.examples | 1 +
debian/rules | 57 ++++
debian/source/format | 1 +
debian/watch | 3 +
18 files changed, 1127 insertions(+)
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..0849e68
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,2 @@
+TODO add global.properties in /etc
+ add alu.properties in examples
diff --git a/debian/alu.properties b/debian/alu.properties
new file mode 100644
index 0000000..9dd160f
--- /dev/null
+++ b/debian/alu.properties
@@ -0,0 +1,41 @@
+[GENERAL]
+######################
+### Initialization ###
+
+db.fullname="alu.n : alu repeat element. alu.a : translation of alu.n repeats"
+db.name=alu
+db.type=nucleic_protein
+
+offline.dir.name=offline/ncbi/blast/alu_tmp
+dir.version=ncbi/blast/alu
+
+frequency.update=0
+
+### Synchronization ###
+
+files.num.threads=1
+
+# NCBI (download fasta)
+protocol=ftp
+server=ftp.ncbi.nih.gov
+remote.dir=/blast/db/FASTA/
+
+release.file=
+release.regexp=
+release.file.compressed=
+
+remote.files=^alu.*\.gz$
+
+#Uncomment if you don't want to extract the data files.
+#no.extract=true
+
+local.files=^alu\.(a|n).*
+
+## Post Process ## The files should be located in the projectfiles/process directory
+
+BLOCKS=
+
+
+### Deployment ###
+# Always keep previous version
+keep.old.version=1
diff --git a/debian/biomaj3-doc.dirs b/debian/biomaj3-doc.dirs
new file mode 100644
index 0000000..69ace7b
--- /dev/null
+++ b/debian/biomaj3-doc.dirs
@@ -0,0 +1 @@
+usr/share/doc/biomaj3-doc
diff --git a/debian/biomaj3-doc.doc-base b/debian/biomaj3-doc.doc-base
new file mode 100644
index 0000000..f9ebf5e
--- /dev/null
+++ b/debian/biomaj3-doc.doc-base
@@ -0,0 +1,10 @@
+Document: biomaj3
+Title: BioMAJ3 Manual
+Author: Olivier Sallou
+Abstract: This manual describes the API of biomaj3
+ and how it can be used.
+Section: Science/Biology
+
+Format: HTML
+Index: /usr/share/doc/biomaj3-doc/html/index.html
+Files: /usr/share/doc/biomaj3-doc/html/*.html
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..83fb0cd
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+python-biomaj3 (3.0.20-1) UNRELEASED; urgency=medium
+
+ * New package (Closes: #NNNN).
+
+ -- Olivier Sallou <osallou at debian.org> Sat, 14 Jan 2017 09:30:04 +0000
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..2f0bd59
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,75 @@
+Source: python-biomaj3
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+Section: python
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ dh-python,
+ python-all,
+ python-all-dev,
+ python-setuptools,
+ python-mock,
+ python-nose,
+ python-pymongo,
+ python-tabulate,
+ python-ldap3,
+ python-bcrypt,
+ python-future,
+ python-elasticsearch,
+ python-pycurl,
+ python-drmaa,
+ python-sphinx,
+ python3-all,
+ python3-all-dev,
+ python3-setuptools,
+ python3-mock,
+ python3-nose,
+ python3-pymongo,
+ python3-tabulate,
+ python3-ldap3,
+ python3-bcrypt,
+ python3-future,
+ python3-elasticsearch,
+ python3-pycurl,
+ python3-sphinx
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-biomaj3.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/python-biomaj3.git
+Homepage: https://github.com/genouest/biomaj
+X-Python-Version: >= 2.7
+X-Python3-Version: >= 3.4
+
+Package: python-biomaj3
+Architecture: any
+Depends: ${misc:Depends},
+ ${python:Depends},
+ ${shlibs:Depends}
+Suggests: mongodb-server, biomaj3-doc
+Description: biological data-bank updater (Python 2)
+ BioMAJ downloads remote data banks, checks their status and applies
+ transformation workflows, with consistent state, to provide ready-to-use
+ data for biologists and bioinformaticians. For example, it can transform
+ original FASTA files into BLAST indexes. It is very flexible and its
+ post-processing facilities can be extended very easily.
+ .
+ This package contains the Python 2 module.
+
+Package: python3-biomaj3
+Architecture: any
+Depends: ${misc:Depends},
+ ${python3:Depends},
+ ${shlibs:Depends}
+Suggests: mongodb-server, biomaj3-doc
+Description: biological data-bank updater (Python 3)
+ BioMAJ downloads remote data banks, checks their status and applies
+ transformation workflows, with consistent state, to provide ready-to-use
+ data for biologists and bioinformaticians. For example, it can transform
+ original FASTA files into BLAST indexes. It is very flexible and its
+ post-processing facilities can be extended very easily.
+ .
+ This package contains the Python 3 module.
+
+Package: biomaj3-doc
+Architecture: all
+Description: API of biomaj3 modules
+ Python documentation of the biomaj3 modules, auto-generated
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..efdf21b
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,687 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: biomaj3
+Source: https://github.com/genouest/biomaj
+
+Files: *
+Copyright: 2015-2016 Olivier Sallou <olivier.sallou at irisa.fr>, IRISA
+License: Affero GPL 3
+ GNU AFFERO GENERAL PUBLIC LICENSE
+ Version 3, 19 November 2007
+ .
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+ organization, or merging organizations. If propagation of a covered
+ work results from an entity transaction, each party to that
+ transaction who receives a copy of the work also receives whatever
+ licenses to the work the party's predecessor in interest had or could
+ give under the previous paragraph, plus a right to possession of the
+ Corresponding Source of the work from the predecessor in interest, if
+ the predecessor has it or can get it with reasonable efforts.
+ .
+ You may not impose any further restrictions on the exercise of the
+ rights granted or affirmed under this License. For example, you may
+ not impose a license fee, royalty, or other charge for exercise of
+ rights granted under this License, and you may not initiate litigation
+ (including a cross-claim or counterclaim in a lawsuit) alleging that
+ any patent claim is infringed by making, using, selling, offering for
+ sale, or importing the Program or any portion of it.
+ .
+ 11. Patents.
+ .
+ A "contributor" is a copyright holder who authorizes use under this
+ License of the Program or a work on which the Program is based. The
+ work thus licensed is called the contributor's "contributor version".
+ .
+ A contributor's "essential patent claims" are all patent claims
+ owned or controlled by the contributor, whether already acquired or
+ hereafter acquired, that would be infringed by some manner, permitted
+ by this License, of making, using, or selling its contributor version,
+ but do not include claims that would be infringed only as a
+ consequence of further modification of the contributor version. For
+ purposes of this definition, "control" includes the right to grant
+ patent sublicenses in a manner consistent with the requirements of
+ this License.
+ .
+ Each contributor grants you a non-exclusive, worldwide, royalty-free
+ patent license under the contributor's essential patent claims, to
+ make, use, sell, offer for sale, import and otherwise run, modify and
+ propagate the contents of its contributor version.
+ .
+ In the following three paragraphs, a "patent license" is any express
+ agreement or commitment, however denominated, not to enforce a patent
+ (such as an express permission to practice a patent or covenant not to
+ sue for patent infringement). To "grant" such a patent license to a
+ party means to make such an agreement or commitment not to enforce a
+ patent against the party.
+ .
+ If you convey a covered work, knowingly relying on a patent license,
+ and the Corresponding Source of the work is not available for anyone
+ to copy, free of charge and under the terms of this License, through a
+ publicly available network server or other readily accessible means,
+ then you must either (1) cause the Corresponding Source to be so
+ available, or (2) arrange to deprive yourself of the benefit of the
+ patent license for this particular work, or (3) arrange, in a manner
+ consistent with the requirements of this License, to extend the patent
+ license to downstream recipients. "Knowingly relying" means you have
+ actual knowledge that, but for the patent license, your conveying the
+ covered work in a country, or your recipient's use of the covered work
+ in a country, would infringe one or more identifiable patents in that
+ country that you have reason to believe are valid.
+ .
+ If, pursuant to or in connection with a single transaction or
+ arrangement, you convey, or propagate by procuring conveyance of, a
+ covered work, and grant a patent license to some of the parties
+ receiving the covered work authorizing them to use, propagate, modify
+ or convey a specific copy of the covered work, then the patent license
+ you grant is automatically extended to all recipients of the covered
+ work and works based on it.
+ .
+ A patent license is "discriminatory" if it does not include within
+ the scope of its coverage, prohibits the exercise of, or is
+ conditioned on the non-exercise of one or more of the rights that are
+ specifically granted under this License. You may not convey a covered
+ work if you are a party to an arrangement with a third party that is
+ in the business of distributing software, under which you make payment
+ to the third party based on the extent of your activity of conveying
+ the work, and under which the third party grants, to any of the
+ parties who would receive the covered work from you, a discriminatory
+ patent license (a) in connection with copies of the covered work
+ conveyed by you (or copies made from those copies), or (b) primarily
+ for and in connection with specific products or compilations that
+ contain the covered work, unless you entered into that arrangement,
+ or that patent license was granted, prior to 28 March 2007.
+ .
+ Nothing in this License shall be construed as excluding or limiting
+ any implied license or other defenses to infringement that may
+ otherwise be available to you under applicable patent law.
+ .
+ 12. No Surrender of Others' Freedom.
+ .
+ If conditions are imposed on you (whether by court order, agreement or
+ otherwise) that contradict the conditions of this License, they do not
+ excuse you from the conditions of this License. If you cannot convey a
+ covered work so as to satisfy simultaneously your obligations under this
+ License and any other pertinent obligations, then as a consequence you may
+ not convey it at all. For example, if you agree to terms that obligate you
+ to collect a royalty for further conveying from those to whom you convey
+ the Program, the only way you could satisfy both those terms and this
+ License would be to refrain entirely from conveying the Program.
+ .
+ 13. Remote Network Interaction; Use with the GNU General Public License.
+ .
+ Notwithstanding any other provision of this License, if you modify the
+ Program, your modified version must prominently offer all users
+ interacting with it remotely through a computer network (if your version
+ supports such interaction) an opportunity to receive the Corresponding
+ Source of your version by providing access to the Corresponding Source
+ from a network server at no charge, through some standard or customary
+ means of facilitating copying of software. This Corresponding Source
+ shall include the Corresponding Source for any work covered by version 3
+ of the GNU General Public License that is incorporated pursuant to the
+ following paragraph.
+ .
+ Notwithstanding any other provision of this License, you have
+ permission to link or combine any covered work with a work licensed
+ under version 3 of the GNU General Public License into a single
+ combined work, and to convey the resulting work. The terms of this
+ License will continue to apply to the part which is the covered work,
+ but the work with which it is combined will remain governed by version
+ 3 of the GNU General Public License.
+ .
+ 14. Revised Versions of this License.
+ .
+ The Free Software Foundation may publish revised and/or new versions of
+ the GNU Affero General Public License from time to time. Such new versions
+ will be similar in spirit to the present version, but may differ in detail to
+ address new problems or concerns.
+ .
+ Each version is given a distinguishing version number. If the
+ Program specifies that a certain numbered version of the GNU Affero General
+ Public License "or any later version" applies to it, you have the
+ option of following the terms and conditions either of that numbered
+ version or of any later version published by the Free Software
+ Foundation. If the Program does not specify a version number of the
+ GNU Affero General Public License, you may choose any version ever published
+ by the Free Software Foundation.
+ .
+ If the Program specifies that a proxy can decide which future
+ versions of the GNU Affero General Public License can be used, that proxy's
+ public statement of acceptance of a version permanently authorizes you
+ to choose that version for the Program.
+ .
+ Later license versions may give you additional or different
+ permissions. However, no additional obligations are imposed on any
+ author or copyright holder as a result of your choosing to follow a
+ later version.
+ .
+ 15. Disclaimer of Warranty.
+ .
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+ APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+ HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+ OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+ THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+ IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+ .
+ 16. Limitation of Liability.
+ .
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+ WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+ THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+ GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+ USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+ DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+ PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+ EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGES.
+ .
+ 17. Interpretation of Sections 15 and 16.
+ .
+ If the disclaimer of warranty and limitation of liability provided
+ above cannot be given local legal effect according to their terms,
+ reviewing courts shall apply local law that most closely approximates
+ an absolute waiver of all civil liability in connection with the
+ Program, unless a warranty or assumption of liability accompanies a
+ copy of the Program in return for a fee.
+ .
+ END OF TERMS AND CONDITIONS
+ .
+ How to Apply These Terms to Your New Programs
+ .
+ If you develop a new program, and you want it to be of the greatest
+ possible use to the public, the best way to achieve this is to make it
+ free software which everyone can redistribute and change under these terms.
+ .
+ To do so, attach the following notices to the program. It is safest
+ to attach them to the start of each source file to most effectively
+ state the exclusion of warranty; and each file should have at least
+ the "copyright" line and a pointer to where the full notice is found.
+ .
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+ .
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as published
+ by the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Affero General Public License for more details.
+ .
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ Also add information on how to contact you by electronic and paper mail.
+ .
+ If your software can interact with users remotely through a computer
+ network, you should also make sure that it provides a way for users to
+ get its source. For example, if your program is a web application, its
+ interface could display a "Source" link that leads users to an archive
+ of the code. There are many ways you could offer source, and different
+ solutions will be better for different programs; see section 13 for the
+ specific requirements.
+ .
+ You should also get your employer (if you work as a programmer) or school,
+ if any, to sign a "copyright disclaimer" for the program, if necessary.
+ For more information on this, and how to apply and follow the GNU AGPL, see
+ <http://www.gnu.org/licenses/>.
+
+Files: debian/*
+Copyright: 2015 Olivier Sallou <osallou at debian.org>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
diff --git a/debian/global.properties-py b/debian/global.properties-py
new file mode 100644
index 0000000..ddfe831
--- /dev/null
+++ b/debian/global.properties-py
@@ -0,0 +1,115 @@
+[GENERAL]
+#The root directory where all databases are stored.
+#If your data is not stored under one directory hirearchy
+#you can override this value in the database properties file.
+data.dir=/var/lib/python-biomaj3/banks
+
+conf.dir=/etc/python-biomaj3/properties
+log.dir=/var/log/python-biomaj3
+process.dir=/etc/python-biomaj3/process
+cache.dir=/var/cache/python-biomaj3
+lock.dir= /var/run/python-biomaj3/lock
+
+db.url=mongodb://localhost:27017
+db.name=biomaj
+
+use_ldap=0
+ldap.host=localhost
+ldap.port=389
+ldap.dn=nodomain
+
+use_elastic=
+#Comma separated list of elasticsearch nodes host1,host2:port2
+elastic_nodes=
+elastic_index=biomaj
+
+# Calculate data.dir size stats
+data.stats=1
+
+# Auto publish on updates (do not need publish flag, can be ovveriden in bank property file)
+auto_publish=0
+
+celery.queue=
+celery.broker=
+########################
+# Global properties file
+
+
+#To override these settings for a specific database go to its
+#properties file and uncomment or add the specific line you want
+#to override.
+
+#----------------
+# Mail Configuration
+#---------------
+#Uncomment thes lines if you want receive mail when the workflow is finished
+
+mail.smtp.host=
+mail.admin=
+mail.from=biomaj at localhost
+mail.user=
+mail.password=
+mail.tls=
+
+
+#Number of thread during the download
+bank.num.threads=4
+
+#Number of threads to use for downloading and processing
+files.num.threads=4
+
+#to keep more than one release increase this value
+keep.old.version=0
+
+#The historic log file is generated in log/
+#define level information for output : DEBUG,INFO,WARN,ERR
+historic.logfile.level=DEBUG
+
+http.parse.dir.line=<a[\\s]+href=\"([\\S]+)/\".*alt=\"\\[DIR\\]\">.*([\\d]{2}-[\\w\\d]{2,5}-[\\d]{4}\\s[\\d]{2}:[\\d]{2})
+http.parse.file.line=<a[\\s]+href=\"([\\S]+)\".*([\\d]{2}-[\\w\\d]{2,5}-[\\d]{4}\\s[\\d]{2}:[\\d]{2})[\\s]+([\\d\\.]+[MKG]{0,1})
+
+http.group.dir.name=1
+http.group.dir.date=2
+http.group.file.name=1
+http.group.file.date=2
+http.group.file.size=3
+
+
+# Bank default access
+visibility.default=public
+
+# Proxy, optional proxy (see format at
+# http://curl.haxx.se/libcurl/c/CURLOPT_PROXY.html)
+# biomaj >= 3.0.7
+#proxy=myproxyhost:1080
+#proxy=myproxyhost
+# Set proxy authentication if any, else keep commented
+#proxy_auth=user:password
+
+[loggers]
+keys = root, biomaj
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level =INFO
+handlers = console
+
+[logger_biomaj]
+level = INFO
+handlers = console
+qualname = biomaj
+propagate=0
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = INFO
+formatter = generic
+
+[formatter_generic]
+format = %(asctime)s %(levelname)-5.5s [%(name)s][%(threadName)s] %(message)s
diff --git a/debian/global.properties-py3 b/debian/global.properties-py3
new file mode 100644
index 0000000..6912141
--- /dev/null
+++ b/debian/global.properties-py3
@@ -0,0 +1,115 @@
+[GENERAL]
+#The root directory where all databases are stored.
+#If your data is not stored under one directory hirearchy
+#you can override this value in the database properties file.
+data.dir=/var/lib/python3-biomaj3/banks
+
+conf.dir=/etc/python3-biomaj3/properties
+log.dir=/var/log/python3-biomaj3
+process.dir=/etc/python3-biomaj3/process
+cache.dir=/var/cache/python3-biomaj3
+lock.dir= /var/run/python3-biomaj3/lock
+
+db.url=mongodb://localhost:27017
+db.name=biomaj
+
+use_ldap=0
+ldap.host=localhost
+ldap.port=389
+ldap.dn=nodomain
+
+use_elastic=
+#Comma separated list of elasticsearch nodes host1,host2:port2
+elastic_nodes=
+elastic_index=biomaj
+
+# Calculate data.dir size stats
+data.stats=1
+
+# Auto publish on updates (do not need publish flag, can be ovveriden in bank property file)
+auto_publish=0
+
+celery.queue=
+celery.broker=
+########################
+# Global properties file
+
+
+#To override these settings for a specific database go to its
+#properties file and uncomment or add the specific line you want
+#to override.
+
+#----------------
+# Mail Configuration
+#---------------
+#Uncomment thes lines if you want receive mail when the workflow is finished
+
+mail.smtp.host=
+mail.admin=
+mail.from=biomaj at localhost
+mail.user=
+mail.password=
+mail.tls=
+
+
+#Number of thread during the download
+bank.num.threads=4
+
+#Number of threads to use for downloading and processing
+files.num.threads=4
+
+#to keep more than one release increase this value
+keep.old.version=0
+
+#The historic log file is generated in log/
+#define level information for output : DEBUG,INFO,WARN,ERR
+historic.logfile.level=DEBUG
+
+http.parse.dir.line=<a[\\s]+href=\"([\\S]+)/\".*alt=\"\\[DIR\\]\">.*([\\d]{2}-[\\w\\d]{2,5}-[\\d]{4}\\s[\\d]{2}:[\\d]{2})
+http.parse.file.line=<a[\\s]+href=\"([\\S]+)\".*([\\d]{2}-[\\w\\d]{2,5}-[\\d]{4}\\s[\\d]{2}:[\\d]{2})[\\s]+([\\d\\.]+[MKG]{0,1})
+
+http.group.dir.name=1
+http.group.dir.date=2
+http.group.file.name=1
+http.group.file.date=2
+http.group.file.size=3
+
+
+# Bank default access
+visibility.default=public
+
+# Proxy, optional proxy (see format at
+# http://curl.haxx.se/libcurl/c/CURLOPT_PROXY.html)
+# biomaj >= 3.0.7
+#proxy=myproxyhost:1080
+#proxy=myproxyhost
+# Set proxy authentication if any, else keep commented
+#proxy_auth=user:password
+
+[loggers]
+keys = root, biomaj
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level =INFO
+handlers = console
+
+[logger_biomaj]
+level = INFO
+handlers = console
+qualname = biomaj
+propagate=0
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = INFO
+formatter = generic
+
+[formatter_generic]
+format = %(asctime)s %(levelname)-5.5s [%(name)s][%(threadName)s] %(message)s
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..e69de29
diff --git a/debian/python-biomaj3.dirs b/debian/python-biomaj3.dirs
new file mode 100644
index 0000000..4a8144b
--- /dev/null
+++ b/debian/python-biomaj3.dirs
@@ -0,0 +1,6 @@
+var/lib/python-biomaj3/banks
+var/log/python-biomaj3
+etc/python-biomaj3/process
+etc/python-biomaj3/properties
+var/cache/python-biomaj3
+var/run/python-biomaj3/lock
diff --git a/debian/python-biomaj3.examples b/debian/python-biomaj3.examples
new file mode 100644
index 0000000..13fe74c
--- /dev/null
+++ b/debian/python-biomaj3.examples
@@ -0,0 +1 @@
+debian/alu.properties
diff --git a/debian/python3-biomaj3.dirs b/debian/python3-biomaj3.dirs
new file mode 100644
index 0000000..3fa5dbd
--- /dev/null
+++ b/debian/python3-biomaj3.dirs
@@ -0,0 +1,6 @@
+var/lib/python3-biomaj3/banks
+var/log/python3-biomaj3
+etc/python3-biomaj3/process
+etc/python3-biomaj3/properties
+var/cache/python3-biomaj3
+var/run/python3-biomaj3/lock
diff --git a/debian/python3-biomaj3.examples b/debian/python3-biomaj3.examples
new file mode 100644
index 0000000..13fe74c
--- /dev/null
+++ b/debian/python3-biomaj3.examples
@@ -0,0 +1 @@
+debian/alu.properties
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..c641a08
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,57 @@
+#!/usr/bin/make -f
+# See debhelper(7) (uncomment to enable)
+# output every command that modifies files on the build system.
+#export DH_VERBOSE = 1
+
+# see EXAMPLES in dpkg-buildflags(1) and read /usr/share/dpkg/*
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+# see FEATURE AREAS in dpkg-buildflags(1)
+# Fails to build when set to +all
+#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
+
+# see ENVIRONMENT in dpkg-buildflags(1)
+# package maintainers to append CFLAGS
+#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
+# package maintainers to append LDFLAGS
+#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+
+export PYBUILD_NAME=biomaj3
+# Skip tests as they need mongodb instance running
+override_dh_auto_test:
+ echo "Skipping tests, they require a running mongodb instance"
+
+# main packaging script based on dh7 syntax
+%:
+ dh $@ --with python2,python3,sphinxdoc --buildsystem=pybuild
+
+override_dh_sphinxdoc:
+ cd docs && make html
+
+override_dh_installdocs:
+ cp -r docs/_build/html debian/biomaj3-doc/usr/share/doc/biomaj3-doc/
+ dh_installdocs
+
+
+override_dh_install:
+ dh_install
+ cp debian/global.properties-py debian/python-biomaj3/etc/python-biomaj3/global.properties
+ cp debian/global.properties-py3 debian/python3-biomaj3/etc/python3-biomaj3/global.properties
+ mv debian/python3-biomaj3/usr/bin/biomaj-cli.py debian/python3-biomaj3/usr/bin/biomaj-cli3
+ mv debian/python-biomaj3/usr/bin/biomaj-cli.py debian/python-biomaj3/usr/bin/biomaj-cli
+
+override_dh_clean:
+ dh_clean
+ rm -rf docs/_build
+
+# help2man fails because python needs to be interpreted
+#override_dh_installman:
+# help2man --no-discard-stderr --version-string="$(DEB_VERSION_UPSTREAM)" -o biomaj-cli3.1 bin/biomaj-cli.py
+# help2man --no-discard-stderr --version-string="$(DEB_VERSION_UPSTREAM)" -o biomaj-cli.1 bin/biomaj-cli.py
+# dh_installman
+
+#override_dh_python3:
+# # skip autoguessa as python3-drmaa is not available but we don't care, code manage case where drmaa is not available
+# dh_python3 -- --no-guessing-deps
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/watch b/debian/watch
new file mode 100644
index 0000000..ca4b2f5
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+opts="repack,compression=xz,filenamemangle=s/.+\/v?(\d\S+)\.tar\.gz/biomaj3-$1\.tar\.gz/" \
+ https://github.com/genouest/biomaj/tags .*/v?(\d\S+)\.tar\.gz
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