Author: moeller Date: 2011-08-25 21:56:01 +0000 (Thu, 25 Aug 2011) New Revision: 7547
Added: trunk/packages/python-pynast/trunk/debian/compat trunk/packages/python-pynast/trunk/debian/manpages trunk/packages/python-pynast/trunk/debian/pynast.1 Removed: trunk/packages/python-pynast/trunk/debian/pyversions Modified: trunk/packages/python-pynast/trunk/debian/README.Debian trunk/packages/python-pynast/trunk/debian/changelog trunk/packages/python-pynast/trunk/debian/control trunk/packages/python-pynast/trunk/debian/docs trunk/packages/python-pynast/trunk/debian/rules Log: Giving python-pynast a spin, getting it out of experimental while doing so (added man page, moving to dh_python2) Once it is in, also qiime can get from experimental to contrib. Modified: trunk/packages/python-pynast/trunk/debian/README.Debian =================================================================== --- trunk/packages/python-pynast/trunk/debian/README.Debian 2011-08-25 21:09:33 UTC (rev 7546) +++ trunk/packages/python-pynast/trunk/debian/README.Debian 2011-08-25 21:56:01 UTC (rev 7547) @@ -3,6 +3,8 @@ Many many thanks got to Jonas from the CDBS team for indicating that I indeed need to set the XB and XS flags for python packages. +A recent update move this all to dh_python2, which does not seem +to need those any more. The package is named -pynast, not -nast, since that is the name of the python module. @@ -12,8 +14,8 @@ a contribtion to upstream and this Debian package by a rudimentary man page would be appreciated. -The documentation is somehow built with the new fancy Free -environment spinx. The packaging should reflect this by adding -spinx as a build-indep dependency, but the packagers have not -yet found the time to address this. Help would be appreciated. - +The package is in need of someone truly loving it. You will be +helped, just raise your hand. + + -- + Steffen Moeller <[email protected]> Thu, 25 Aug 2011 23:31:25 +0200 Modified: trunk/packages/python-pynast/trunk/debian/changelog =================================================================== --- trunk/packages/python-pynast/trunk/debian/changelog 2011-08-25 21:09:33 UTC (rev 7546) +++ trunk/packages/python-pynast/trunk/debian/changelog 2011-08-25 21:56:01 UTC (rev 7547) @@ -1,3 +1,12 @@ +python-pynast (1.1-2) unstable; urgency=low + + * Transition to dh7 and dh_python2 + * Adjusted uploaders, first upload to unstable + * Documentation built with sphinx + * Added man page + + -- Steffen Moeller <[email protected]> Thu, 25 Aug 2011 23:19:06 +0200 + python-pynast (1.1-1) experimental; urgency=low * Initial release (Closes: #587189) Added: trunk/packages/python-pynast/trunk/debian/compat =================================================================== --- trunk/packages/python-pynast/trunk/debian/compat (rev 0) +++ trunk/packages/python-pynast/trunk/debian/compat 2011-08-25 21:56:01 UTC (rev 7547) @@ -0,0 +1 @@ +7 Modified: trunk/packages/python-pynast/trunk/debian/control =================================================================== --- trunk/packages/python-pynast/trunk/debian/control 2011-08-25 21:09:33 UTC (rev 7546) +++ trunk/packages/python-pynast/trunk/debian/control 2011-08-25 21:56:01 UTC (rev 7547) @@ -2,19 +2,18 @@ Section: contrib/python Priority: extra Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Sri Girish Srinivasa Murthy <[email protected]>, Steffen Moeller <[email protected]> -Build-Depends: debhelper (>= 7), cdbs, python (>= 2.5), python-central, python-cogent +Uploaders: Steffen Moeller <[email protected]> +Build-Depends: debhelper (>= 7), python (>= 2.6.6-3~), python-central, python-cogent, python-sphinx XS-Autobuild: yes -Standards-Version: 3.9.0 +Standards-Version: 3.9.2 Homepage: http://pynast.sourceforge.net/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/python-nast/trunk/?rev=0&sc=0 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/python-nast/trunk/ -XS-Python-Version: >= 2.5 +X-Python-Version: >= 2.5 Package: python-pynast Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends} -XB-Python-Version: ${python:Versions} Description: alignment of short DNA sequences The package provices a reimplementation of the Nearest Alignment Space Termination tool in python. It was prepared for next generation Modified: trunk/packages/python-pynast/trunk/debian/docs =================================================================== --- trunk/packages/python-pynast/trunk/debian/docs 2011-08-25 21:09:33 UTC (rev 7546) +++ trunk/packages/python-pynast/trunk/debian/docs 2011-08-25 21:56:01 UTC (rev 7547) @@ -1,2 +1,2 @@ README -doc/* +doc/_build/html Added: trunk/packages/python-pynast/trunk/debian/manpages =================================================================== --- trunk/packages/python-pynast/trunk/debian/manpages (rev 0) +++ trunk/packages/python-pynast/trunk/debian/manpages 2011-08-25 21:56:01 UTC (rev 7547) @@ -0,0 +1 @@ +debian/pynast.1 Added: trunk/packages/python-pynast/trunk/debian/pynast.1 =================================================================== --- trunk/packages/python-pynast/trunk/debian/pynast.1 (rev 0) +++ trunk/packages/python-pynast/trunk/debian/pynast.1 2011-08-25 21:56:01 UTC (rev 7547) @@ -0,0 +1,62 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4. .. and only minimally edited +.TH VERSION: "1" "August 2011" "Version: pynast 1.1" "User Commands" +.SH NAME +PyNAST \- alignment of short DNA sequences +.SH SYNOPSIS +.B pynast +[\fIoptions\fR] \fI{-i input_fp -t template_fp}\fR +.SH DESCRIPTION +[] indicates optional input (order unimportant) +{} indicates required input (order unimportant) +.SS "Example usage:" +.IP +pynast \fB\-i\fR my_input.fasta \fB\-t\fR my_template.fasta +.SH OPTIONS +.TP +\fB\-\-version\fR +show program's version number and exit +.TP +\fB\-h\fR, \fB\-\-help\fR +show this help message and exit +.TP +\fB\-t\fR TEMPLATE_FP, \fB\-\-template_fp\fR=\fITEMPLATE_FP\fR +path to template alignment file [REQUIRED] +.TP +\fB\-i\fR INPUT_FP, \fB\-\-input_fp\fR=\fIINPUT_FP\fR +path to input fasta file [REQUIRED] +.TP +\fB\-v\fR, \fB\-\-verbose\fR +Print status and other information during execution +[default: False] +.TP +\fB\-p\fR MIN_PCT_ID, \fB\-\-min_pct_id\fR=\fIMIN_PCT_ID\fR +minimum percent sequence identity to consider a +sequence a match [default: 75.0] +.TP +\fB\-l\fR MIN_LEN, \fB\-\-min_len\fR=\fIMIN_LEN\fR +minimum sequence length to include in NAST alignment +[default: 1000] +.TP +\fB\-m\fR PAIRWISE_ALIGNMENT_METHOD, \fB\-\-pairwise_alignment_method\fR=\fIPAIRWISE_ALIGNMENT_METHOD\fR +method for performing pairwise alignment [default: +uclust] +.TP +\fB\-a\fR FASTA_OUT_FP, \fB\-\-fasta_out_fp\fR=\fIFASTA_OUT_FP\fR +path to store resulting alignment file [default: +derived from input filepath] +.TP +\fB\-g\fR LOG_FP, \fB\-\-log_fp\fR=\fILOG_FP\fR +path to store log file [default: derived from input +filepath] +.TP +\fB\-f\fR FAILURE_FP, \fB\-\-failure_fp\fR=\fIFAILURE_FP\fR +path to store file of seqs which fail to align +[default: derived from input filepath] +.TP +\fB\-e\fR MAX_E_VALUE, \fB\-\-max_e_value\fR=\fIMAX_E_VALUE\fR +Depreciated. Will be removed in PyNAST 1.2 +.TP +\fB\-d\fR BLAST_DB, \fB\-\-blast_db\fR=\fIBLAST_DB\fR +Depreciated. Will be removed in PyNAST 1.2 +.SH "SEE ALSO" +http://pynast.sourceforge.net Deleted: trunk/packages/python-pynast/trunk/debian/pyversions =================================================================== --- trunk/packages/python-pynast/trunk/debian/pyversions 2011-08-25 21:09:33 UTC (rev 7546) +++ trunk/packages/python-pynast/trunk/debian/pyversions 2011-08-25 21:56:01 UTC (rev 7547) @@ -1 +0,0 @@ -all Modified: trunk/packages/python-pynast/trunk/debian/rules =================================================================== --- trunk/packages/python-pynast/trunk/debian/rules 2011-08-25 21:09:33 UTC (rev 7546) +++ trunk/packages/python-pynast/trunk/debian/rules 2011-08-25 21:56:01 UTC (rev 7547) @@ -4,9 +4,14 @@ # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 -export DEB_PYTHON_SYSTEM=pycentral -include /usr/share/cdbs/1/rules/debhelper.mk -include /usr/share/cdbs/1/class/python-distutils.mk +#include /usr/share/cdbs/1/rules/debhelper.mk +#include /usr/share/cdbs/1/class/python-distutils.mk +%: + dh $@ --with python2 + +build-indep: + $(MAKE) -C doc html + clean:: rm -rf build build-stamp _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
