Author: tbooth-guest Date: 2011-03-24 17:18:25 +0000 (Thu, 24 Mar 2011) New Revision: 6379
Added: trunk/packages/qiime/trunk/debian/scripts/uclust Modified: trunk/packages/qiime/trunk/debian/changelog trunk/packages/qiime/trunk/debian/control trunk/packages/qiime/trunk/debian/rules trunk/packages/qiime/trunk/debian/scripts/qiime trunk/packages/qiime/trunk/debian/scripts/shell/qiime_help Log: Pushing a few more changes for the day. Awaiting feedback from Bio-Linux testers. Still a work in progress. Modified: trunk/packages/qiime/trunk/debian/changelog =================================================================== --- trunk/packages/qiime/trunk/debian/changelog 2011-03-24 15:09:19 UTC (rev 6378) +++ trunk/packages/qiime/trunk/debian/changelog 2011-03-24 17:18:25 UTC (rev 6379) @@ -1,3 +1,16 @@ +qiime (1.2.1-ubuntu5) lucid; urgency=low + + * Fixed silly error in qiime wrapper script + * Added uclust wrapper to deal with uclust being expected but missing + + -- Tim Booth <[email protected]> Thu, 24 Mar 2011 16:52:43 +0000 + +qiime (1.2.1-ubuntu4) lucid; urgency=low + + * Fixed dependency - needs python-cogent >= 1.5 + + -- Tim Booth <[email protected]> Thu, 24 Mar 2011 15:33:03 +0000 + qiime (1.2.1-ubuntu3) lucid; urgency=low * Moved .py scripts out of /usr/bin Modified: trunk/packages/qiime/trunk/debian/control =================================================================== --- trunk/packages/qiime/trunk/debian/control 2011-03-24 15:09:19 UTC (rev 6378) +++ trunk/packages/qiime/trunk/debian/control 2011-03-24 17:18:25 UTC (rev 6379) @@ -2,7 +2,7 @@ Section: contrib/science Priority: extra Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Sri Girish Srinivasa Murthy <[email protected]>, Steffen Moeller <[email protected]> +Uploaders: Sri Girish Srinivasa Murthy <[email protected]>, Steffen Moeller <[email protected]>, Tim Booth <[email protected]> Build-Depends: debhelper (>= 7), cdbs, python, python-central, python-cogent, python-numpy, python-matplotlib Standards-Version: 3.9.1 Homepage: http://qiime.sourceforge.net/ @@ -12,7 +12,7 @@ Package: qiime Architecture: all -Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}, python-pynast +Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}, python-pynast, python-cogent ( >= 1.5 ) Recommends: blast2, cd-hit, denoiser, rdp-classifier, chimeraslayer, muscle, infernal, fasttree Suggests: t-coffee, cytoscape Conflicts: bio-linux-qiime (<= bl1.1.x) Modified: trunk/packages/qiime/trunk/debian/rules =================================================================== --- trunk/packages/qiime/trunk/debian/rules 2011-03-24 15:09:19 UTC (rev 6378) +++ trunk/packages/qiime/trunk/debian/rules 2011-03-24 17:18:25 UTC (rev 6379) @@ -13,6 +13,8 @@ export ROOTDIR=debian/`dh_listpackages` # Apparently the override_dh_* mechanism doesn't work with the above includes?? +# Yes, see http://lists.debian.org/debian-med/2011/03/msg00211.html +# TODO - redo this file as Andreas suggested. clean:: rm -rf doc/_build @@ -27,7 +29,9 @@ install -m 755 -d $(ROOTDIR)/etc/qiime mv $(ROOTDIR)/usr/bin/*.py $(ROOTDIR)/usr/lib/qiime/bin install -m 755 debian/scripts/qiime $(ROOTDIR)/usr/bin + install -m 755 debian/scripts/uclust $(ROOTDIR)/usr/lib/qiime/bin cp -R --no-preserve=all debian/scripts/shell $(ROOTDIR)/usr/lib/qiime + rm -r $(ROOTDIR)/usr/lib/qiime/shell/.svn chmod -R a+rX $(ROOTDIR)/usr/lib/qiime/shell install -m 644 debian/scripts/qiime_config $(ROOTDIR)/etc/qiime/qiime_config # Lintian complains about case of ChangeLog.gz Modified: trunk/packages/qiime/trunk/debian/scripts/qiime =================================================================== --- trunk/packages/qiime/trunk/debian/scripts/qiime 2011-03-24 15:09:19 UTC (rev 6378) +++ trunk/packages/qiime/trunk/debian/scripts/qiime 2011-03-24 17:18:25 UTC (rev 6379) @@ -16,7 +16,7 @@ QIIMESHELL="$SHELL --rcfile /usr/lib/qiime/shell/.bashrc" QSNAME="BASH ($SHELL)" else - if [ which bash > /dev/null ] ; then + if which bash > /dev/null ; then QIIMESHELL="bash --rcfile /usr/lib/qiime/shell/.bashrc" QSNAME="BASH" else Modified: trunk/packages/qiime/trunk/debian/scripts/shell/qiime_help =================================================================== --- trunk/packages/qiime/trunk/debian/scripts/shell/qiime_help 2011-03-24 15:09:19 UTC (rev 6378) +++ trunk/packages/qiime/trunk/debian/scripts/shell/qiime_help 2011-03-24 17:18:25 UTC (rev 6379) @@ -1,16 +1,47 @@ -This is the old help text - file locations are wrong - needs re-writing... +This is a proto-manpage for Qiime on Debian/Bio-Linux. +Some of this info alternatively belongs in README.Debian. -Welcome to Qiime on Bio-Linux. -You can now type any of the qiime commands at the qiime prompt. +INVOCATION: -For certain qiime commands, you need to indicate where your qiime parameters file is. You should make a copy of the default version at /usr/local/bioinf/qiime/qiime/qiime_parameters.txt and edit it to suit your needs. A key thing to edit is the location of your greengenes database and lanemask files. + To run a Qiime command such as check_id_map.py: -You either need to have your edited copy of your qiime parameter file in your working directory, or you need to give the path to the file using the -p parameter in the relevant qiime commands. + % qiime check_id_map [...] -IMPORTANT: Please make sure that you have copies of the greengenes core set data file (fasta) and the greengenes alignment lanemask file installed. These do NOT come with the bio-linux-qiime package. You must edit your custom parameter file in your working directory to give the full path to these files. + or just type 'qiime' to get a shell environment where all Qiime commands are available, ie: -Your QIIME_CONFIG_FP is set to /usr/local/bioinf/qiime/qiime/bl_qiime_config. It is unlikely you will need to change the settings in this file. + % qiime + % qiime > check_id_map.py [...] +PARAMETERS FILE: + + For certain qiime commands, you need to indicate where your qiime parameters file is. You + should make a copy of the default version at /usr/share/doc/qiime/qiime_parameters.txt and + edit it to suit your needs. A key thing to edit is the location of your greengenes + database and lanemask files. + + You either need to have your edited copy of your qiime parameter file in your working + directory, or you need to give the path to the file using the -p parameter in the relevant + qiime commands. + +GREENGENES DATA: + + Make sure that you have copies of the greengenes core set data file (fasta) and the + greengenes alignment lanemask file installed. These do NOT come with the bio-linux-qiime + package. You must edit your custom parameter file in your working directory to give the + full path to these files. + +QIIME CONFIGURATION: + + Qiime reads configuration information from the file specified by QIIME_CONFIG_FP. + Your QIIME_CONFIG_FP is set to /etc/qiime/qiime_config. It is unlikely you will need to + change the settings in this file. + +UCLUST: + + You may need to install UClust manually to use some Qiime functions. + For more info, try running 'uclust' at the qiime prompt. + + For more information about Qiime, please refer to the Qiime documentation at: -http://qiime.sourceforge.net/ + http://qiime.sourceforge.net/ Added: trunk/packages/qiime/trunk/debian/scripts/uclust =================================================================== --- trunk/packages/qiime/trunk/debian/scripts/uclust (rev 0) +++ trunk/packages/qiime/trunk/debian/scripts/uclust 2011-03-24 17:18:25 UTC (rev 6379) @@ -0,0 +1,32 @@ +#!/bin/sh +# +# Added by Tim Booth <[email protected]> +# Qiime wants very much to use the UClust binary, but this is not free software. +# However, it is available right now free-of-charge if: +# a) You are an academic user and only want the 32-bit version. +# b) You promise to use the UClust application only as part of Qiime. +# +# My plan is to put the no-cost UClust into bio-linux-qiime. If someone +# installs just the reglar qiime package they need to know what to do... + +# See if uclust.real is available. +if which uclust.real >/dev/null ; then + exec uclust.real "$@" +fi + +if [ `uname -m` = x86_64 ] ; then + bits='64-bit' +else + bits='32-bit' +fi + +echo """\ +UClust is not freely redistributable and is thus not included in the default Qiime package. + +To use this feature, please go to: + http://www.drive5.com/uclust/downloads1_2_21q.html + +Download the $bits binary, then: + sudo cp uclustq1.2.21_* /usr/local/bin/uclust + sudo chmod a+x /usr/local/bin/uclust +""" _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
