[med-svn] r6379 - in trunk/packages/qiime/trunk/debian: . scripts scripts/shell
Timothy Booth
tbooth-guest at alioth.debian.org
Thu Mar 24 17:18:30 UTC 2011
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 <tbooth at ceh.ac.uk> 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 <tbooth at ceh.ac.uk> 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 <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>, Steffen Moeller <moeller at debian.org>
+Uploaders: Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>, Steffen Moeller <moeller at debian.org>, Tim Booth <tbooth at ceh.ac.uk>
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 <tbooth at ceh.ac.uk>
+# 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
+"""
More information about the debian-med-commit
mailing list