[med-svn] r7575 - in trunk/packages/qiime: . branches branches/lucid branches/lucid/debian branches/lucid/debian/patches branches/lucid/debian/scripts branches/lucid/debian/scripts/shell branches/lucid/debian/source
Andreas Tille
tille at alioth.debian.org
Mon Aug 29 09:02:22 UTC 2011
Author: tille
Date: 2011-08-29 09:02:22 +0000 (Mon, 29 Aug 2011)
New Revision: 7575
Added:
trunk/packages/qiime/branches/
trunk/packages/qiime/branches/lucid/
trunk/packages/qiime/branches/lucid/debian/
trunk/packages/qiime/branches/lucid/debian/README.Debian
trunk/packages/qiime/branches/lucid/debian/README.source
trunk/packages/qiime/branches/lucid/debian/changelog
trunk/packages/qiime/branches/lucid/debian/compat
trunk/packages/qiime/branches/lucid/debian/conffiles
trunk/packages/qiime/branches/lucid/debian/control
trunk/packages/qiime/branches/lucid/debian/copyright
trunk/packages/qiime/branches/lucid/debian/dirs
trunk/packages/qiime/branches/lucid/debian/docs
trunk/packages/qiime/branches/lucid/debian/install
trunk/packages/qiime/branches/lucid/debian/patches/
trunk/packages/qiime/branches/lucid/debian/patches/fix_shebang_lines.patch
trunk/packages/qiime/branches/lucid/debian/patches/python26_trim_sff_primers.patch
trunk/packages/qiime/branches/lucid/debian/patches/series
trunk/packages/qiime/branches/lucid/debian/rules
trunk/packages/qiime/branches/lucid/debian/scripts/
trunk/packages/qiime/branches/lucid/debian/scripts/qiime
trunk/packages/qiime/branches/lucid/debian/scripts/qiime_config
trunk/packages/qiime/branches/lucid/debian/scripts/shell/
trunk/packages/qiime/branches/lucid/debian/scripts/shell/.bashrc
trunk/packages/qiime/branches/lucid/debian/scripts/shell/.zshrc
trunk/packages/qiime/branches/lucid/debian/scripts/shell/qiime_environment
trunk/packages/qiime/branches/lucid/debian/scripts/shell/qiime_help
trunk/packages/qiime/branches/lucid/debian/scripts/uclust
trunk/packages/qiime/branches/lucid/debian/source/
trunk/packages/qiime/branches/lucid/debian/source/format
trunk/packages/qiime/branches/lucid/debian/watch
Removed:
trunk/packages/qiime/trunk_debhelper/
Log:
Bring back lucid branch - sorry for the confusion
Added: trunk/packages/qiime/branches/lucid/debian/README.Debian
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/README.Debian (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/README.Debian 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,52 @@
+Quick Start
+===========
+
+Type 'qiime' at the shell prompt before running any of the standard
+qiime commands.
+
+QIIME for Debian and Ubuntu
+===========================
+
+QIIME is a very powerful environment, but the core of its power stems
+from the tools underneath.
+
+Not all those tools that QIIME can work with are yet available with
+Debian. If you find resources to help - please do.
+
+Most of the needed tools are available via the Bio-Linux project:
+http://nebc.nerc.ac.uk/tools/bio-linux . This package was one of the
+first to profit from now joint forces on getting the packages to a
+best-possible shape for everyone.
+
+The package is in experimental since:
+ * it depends on python-pynast that is in experimental - and since like
+ pynast it uses the sphinx documentation system that it not yet uses
+ to streamline the orig.tar.gz and recreate the documentation from
+ its sources. When adding python-sphinx the build fails because of
+ a conflict to orig.tar.gz that could not yet be resolved.
+ * qiime still lacks a man page
+
+The distribution is set to contrib because of
+ * the strong recommends to use uclust that is not shipped with
+ Debian as a binary only package.
+
+
+Disambiguation of versions in bio-linux, Debian and Ubuntu
+----------------------------------------------------------
+
+The conflict reports in the control file is originally indiciated against
+bio-linux-qiime (<= bl1.1.x). The prefix "bl" is unfortunate since the
+Debian packaging tools demand (and the Debian policy) demand the version
+to start with a number, not a character. The version is now removed from
+that indicated conflict.
+
+Depending on who was performing the last editing of the package, versions
+are either specified with a suffix "-N", N numeric, for uploads to Debian,
+or with the suffix "-ubuntuN". The changelog shall show the Ns to increase
+and be reset for new upstream versions. This is yet slightly different
+from the common practice to have the Ubuntu vesion keep the last Debian
+version (or start a new one as 0) and have the version extended to
+"NubuntuM" with M reset to 1 with every new Debian version. Either way
+makes sense. The current approach indiciates better that some upload
+to Debian may not yet have happened.
+
Added: trunk/packages/qiime/branches/lucid/debian/README.source
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/README.source (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/README.source 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,46 @@
+QIIME for Debian - source
+=========================
+
+.py endings and the qiime wrapper of Bio-Linux
+----------------------------------------------
+
+Previous comment by Steffen:
+
+Lintian complains a lot about script-with-language-extension,
+i.e. the .py endings for files ending up in /usr/bin.
+What to do about this is not clear for the moment. For the
+time speaking it seems like lintian is wrong here, too deeply
+embedded is python in the project and Debian does not
+want to become incompatible.
+
+New comments by Tim:
+
+I borrowed the Bio-Linux approach for Qiime which may or may not be the best idea.
+Essentially, the Python scripts are not in the path and instead of running:
+
+% my_qiime_app.py
+
+You run:
+
+% qiime my_qiime_app.py
+
+or equivalently just:
+
+% qiime my_qiime_app
+
+The 'qiime' wrapper script adds the extension if needed and sets the path. If run with
+no arguments it sets the path and drops to an interactive shell.
+
+The dependencies of Qiime essentially make it non-free despite the DFSG licence on the Qiime
+code itself. Chief among these is UClust. This package is supposed to handle the lack of UClust
+gracefully but it is still up to the user to fetch and install it.
+
+Other dependencies/TODO:
+------------------------
+
+Everything else needed should be packaged, if not in Debian proper then in the SVN.
+
+denoiser - no longer a dependency as it has been folded into Qiime itself.
+several recommended deps should probably be hard depends, as long as they are available in the archive
+
+
Added: trunk/packages/qiime/branches/lucid/debian/changelog
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/changelog (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/changelog 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,77 @@
+qiime (1.3.0-1) unstable; urgency=low
+
+ * Bringing qiime to Debian
+ [Steffen]
+ * Some reformatting of debian/control
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Fri, 26 Aug 2011 17:48:30 +0200
+
+qiime (1.3.0-0ubuntu5) lucid; urgency=low
+
+ * Very minor fix to scripts/shell/qiime_environment
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Tue, 16 Aug 2011 12:35:06 +0100
+
+qiime (1.3.0-0ubuntu4) lucid; urgency=low
+
+ * New upstream release. Needs newer Python-Cogent
+ and includes built-in denoiser, so I have now aliased
+ denoiser to run the qiime wrapper.
+ * As the upstream now contains a tiny compiled package I've had
+ to make it arch dependent (support_files/denoiser/FlowgramAlignment
+ code written in Haskell).
+ * Added build dep on ghc6 for the same reson
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Tue, 19 Jul 2011 17:38:28 +0100
+
+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
+ * Added /usr/bin/qiime wrapper script as per Bio-Linux
+ * Added default configuration file
+ * Cleaned up documentation
+ * Added many dependencies (some of which are still not packaged)
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Thu, 24 Mar 2011 11:35:58 +0000
+
+qiime (1.2.1-ubuntu2) lucid; urgency=low
+
+ * Pulled 1.2.1 source and tried a rebuild.
+ * Fixed Lintian changelog warning.
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Tue, 22 Mar 2011 13:55:49 +0000
+
+qiime (1.2.1-2) experimental; urgency=low
+
+ * Initial release (Closes: #587275)
+ * Fixed Python 2.6 incompatibility.
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 02 Mar 2011 22:33:45 +0100
+
+qiime (1.2.1-1) experimental; urgency=low
+
+ * Corrected home page
+ * Updated policy to 3.9.1
+ * Updated debian/README.Debian
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 02 Mar 2011 18:19:39 +0100
+
+qiime (1.1.0-1) experimental; urgency=low
+
+ * Initial release.
+
+ -- Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de> Tue, 20 Jul 2010 00:03:02 +0200
+
Added: trunk/packages/qiime/branches/lucid/debian/compat
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/compat (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/compat 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1 @@
+5
Added: trunk/packages/qiime/branches/lucid/debian/conffiles
===================================================================
Added: trunk/packages/qiime/branches/lucid/debian/control
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/control (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/control 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,55 @@
+Source: qiime
+Section: contrib/science
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>, Tim Booth <tbooth at ceh.ac.uk>
+Build-Depends: debhelper (>= 8), cdbs, python, python-central, python-cogent ( >= 1.5.1 ), python-numpy, python-matplotlib, ghc6
+Standards-Version: 3.9.2
+Homepage: http://qiime.sourceforge.net/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/qiime/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/qiime/trunk/
+XS-Python-Version: >= 2.6
+
+Package: qiime
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}, python-pynast (>= 1.1)|pynast (>= 1.1), python-cogent ( >= 1.5.1 )
+Recommends: blast2 | blast+-legacy, cd-hit, rdp-classifier, chimeraslayer, muscle, infernal, fasttree, ampliconnoise, python-matplotlib, python-numpy
+Conflicts: denoiser
+Replaces: denoiser
+#Provides: denoiser # matter of discussion
+Suggests: t-coffee, cytoscape
+XB-Python-Version: ${python:Versions}
+Description: Quantitative Insights Into Microbial Ecology
+ QIIME (canonically pronounced ‘Chime’) is a pipeline for performing
+ microbial community analysis that integrates many third party tools which
+ have become standard in the field. A standard QIIME analysis begins with
+ sequence data from one or more sequencing platforms, including
+ * Sanger,
+ * Roche/454, and
+ * Illumina GAIIx.
+ With all the underlying tools installed,
+ of which not all are yet available in Debian (or any other Linux
+ distribution), QIIME can perform
+ * library de-multiplexing and quality filtering;
+ * denoising with PyroNoise;
+ * OTU and representative set picking with uclust, cdhit, mothur, BLAST,
+ or other tools;
+ * taxonomy assignment with BLAST or the RDP classifier;
+ * sequence alignment with PyNAST, muscle, infernal, or other tools;
+ * phylogeny reconstruction with FastTree, raxml, clearcut, or other tools;
+ * alpha diversity and rarefaction, including visualization of results,
+ using over 20 metrics including Phylogenetic Diversity, chao1, and
+ observed species;
+ * beta diversity and rarefaction, including visualization of results,
+ using over 25 metrics including weighted and unweighted UniFrac,
+ Euclidean distance, and Bray-Curtis;
+ * summarization and visualization of taxonomic composition of samples
+ using pie charts and histograms
+ and many other features.
+ .
+ QIIME includes parallelization capabilities for many of the
+ computationally intensive steps. By default, these are configured to
+ utilize a mutli-core environment, and are easily configured to run in
+ a cluster environment. QIIME is built in Python using the open-source
+ PyCogent toolkit. It makes extensive use of unit tests, and is highly
+ modular to facilitate custom analyses.
Added: trunk/packages/qiime/branches/lucid/debian/copyright
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/copyright (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/copyright 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,28 @@
+This work was packaged for Debian by:
+
+ Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>
+ and Steffen Moeller <moeller at debian.org>
+ on Fri, 25 Jun 2010 17:23:58 +0200
+
+It was downloaded from <http://pynast.sorceforge.net>
+
+Upstream Author:
+
+ Greg Caporaso <gregcaporaso at gmail.com>
+ Kyle Bittinger
+
+Copyright:
+
+ Copyright 2010, The QIIME Project
+
+License:
+
+ GPL-2
+
+The Debian packaging is:
+
+ Copyright (C) 2010 Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>
+ and Steffen Moeller <moeller at debian.org>
+
+and is licensed under the same copyright,
+see `/usr/share/common-licenses/GPL-2'.
Added: trunk/packages/qiime/branches/lucid/debian/dirs
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/dirs (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/dirs 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,2 @@
+usr/lib/qiime/bin
+etc/qiime
Added: trunk/packages/qiime/branches/lucid/debian/docs
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/docs (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/docs 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,5 @@
+README
+qiime_parameters.txt
+qiime_tutorial/
+doc/_build/*
+doc/vb_files
Added: trunk/packages/qiime/branches/lucid/debian/install
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/install (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/install 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,3 @@
+debian/scripts/qiime usr/bin
+debian/scripts/shell usr/lib/qiime
+debian/scripts/qiime_config etc/qiime/qiime_config
Added: trunk/packages/qiime/branches/lucid/debian/patches/fix_shebang_lines.patch
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/patches/fix_shebang_lines.patch (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/patches/fix_shebang_lines.patch 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,8 @@
+--- a/scripts/denoiser_postprocess.py
++++ b/scripts/denoiser_postprocess.py
+@@ -1,4 +1,4 @@
+- #!/usr/bin/env python
++#!/usr/bin/python
+
+ __author__ = "Jens Reeder"
+ __copyright__ = "Copyright 2011, The QIIME Project"
Added: trunk/packages/qiime/branches/lucid/debian/patches/python26_trim_sff_primers.patch
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/patches/python26_trim_sff_primers.patch (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/patches/python26_trim_sff_primers.patch 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,15 @@
+Index: Qiime-1.2.1/qiime/trim_sff_primers.py
+===================================================================
+--- Qiime-1.2.1.orig/qiime/trim_sff_primers.py 2011-03-02 22:27:48.000000000 +0100
++++ Qiime-1.2.1/qiime/trim_sff_primers.py 2011-03-02 22:29:00.000000000 +0100
+@@ -101,8 +101,8 @@
+ clipped_header, clipped_reads = set_clip_qual_left(sff_data, readlength)
+
+ _, temp_fp = tempfile.mkstemp(dir=sff_dir)
+- with open(temp_fp, 'w') as f:
+- write_binary_sff(f, clipped_header, clipped_reads)
++ f = open(temp_fp, 'w')
++ write_binary_sff(f, clipped_header, clipped_reads)
+
+ shutil.move(temp_fp, sff_fp)
+
Added: trunk/packages/qiime/branches/lucid/debian/patches/series
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/patches/series (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/patches/series 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,2 @@
+python26_trim_sff_primers.patch
+fix_shebang_lines.patch
Added: trunk/packages/qiime/branches/lucid/debian/rules
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/rules (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/rules 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,49 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+#
+# FIXME - don't edit this file any more. Pull Steffen's version and work from there.
+# Except that won't work with Ubuntu 10.04 so we're stuffed.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+export DEB_PYTHON_SYSTEM=pycentral
+export DEB_COMPRESS_EXCLUDE=.js .sff .qual .fna .fna.txt
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/python-distutils.mk
+
+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/*
+ ( cd qiime/support_files/denoiser/FlowgramAlignment && make clean ) || true
+ rm -f qiime/support_files/denoiser/bin/*
+
+#Lots of shuffling to be done...
+# Python scripts go into /usr/lib/qiime/bin (not /usr/bin)
+# Helper script goes into /usr/bin
+# Setup scripts go into /usr/lib/qiime/shell
+# Default configuration goes into /etc/qiime/default_qiime_config
+# ...or maybe it should be copied to $HOME/.qiime_config on 1st run?
+# Since 3.0, denoiser is aliased to Qiime
+common-binary-fixup-arch::
+ install -m 755 -d $(ROOTDIR)/usr/lib/qiime/bin
+ 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
+ ln -sf qiime $(ROOTDIR)/usr/bin/denoiser
+ install -m 755 debian/scripts/uclust $(ROOTDIR)/usr/lib/qiime/bin
+ cp -R --no-preserve=all debian/scripts/shell $(ROOTDIR)/usr/lib/qiime
+ rm -rf $(ROOTDIR)/usr/lib/qiime/shell/.svn
+ chmod -R a+rX $(ROOTDIR)/usr/lib/qiime/shell
+ chmod -R go-w $(ROOTDIR)/usr/lib/qiime/shell
+ rm -rf $(ROOTDIR)/etc/qiime/qiime_config
+ install -m 644 debian/scripts/qiime_config $(ROOTDIR)/etc/qiime/qiime_config
+ # Lintian complains about case of ChangeLog.gz
+ ( cd $(ROOTDIR)/usr/share/doc/`dh_listpackages` ; mv ChangeLog.gz changelog.gz || true )
+ # And about the existence of /usr/qiime
+ mv $(ROOTDIR)/usr/qiime/support_files $(ROOTDIR)/usr/lib/qiime && rmdir $(ROOTDIR)/usr/qiime
Property changes on: trunk/packages/qiime/branches/lucid/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/qiime/branches/lucid/debian/scripts/qiime
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/scripts/qiime (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/scripts/qiime 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,48 @@
+#!/bin/sh
+
+# Set up a Qiime working environment. This should either run the Qiime command directly
+# or else drop the user to a shell where Qiime is ready to run.
+# For now, if $SHELL is zsh use that, otherwise run bash.
+
+if [ "$*" = "" ] ; then
+ #Run a shell
+ if [ `basename "$SHELL"` = "zsh" ] ; then
+ export ZOLDDOTDIR=${ZSHDOTDIR:-~}
+ export ZDOTDIR=/usr/lib/qiime/shell
+ QIIMESHELL="$SHELL"
+ QSNAME="ZSH ($SHELL)"
+ elif [ `basename "$SHELL"` = "bash" ] ; then
+ #Set bash dot directory.
+ QIIMESHELL="$SHELL --rcfile /usr/lib/qiime/shell/.bashrc"
+ QSNAME="BASH ($SHELL)"
+ else
+ if which bash > /dev/null ; then
+ QIIMESHELL="bash --rcfile /usr/lib/qiime/shell/.bashrc"
+ QSNAME="BASH"
+ else
+ #This should never happen due to package dependencies.
+ echo "To start an interactive Qiime shell, you need to have 'bash' available and"
+ echo "in your path."
+ exit 1
+ fi
+ fi
+
+echo """
+Setting up $QSNAME environment to run Qiime commands.
+
+Type 'help' for more info, 'exit' to return to regular shell.
+"""
+
+ eval exec $QIIMESHELL
+
+else
+ #Just run the command
+
+ # Set environment
+ . /usr/lib/qiime/shell/qiime_environment
+
+ cmd=`basename "$1" .py`.py
+ shift
+
+ exec "/usr/lib/qiime/bin/$cmd" "$@"
+fi
Added: trunk/packages/qiime/branches/lucid/debian/scripts/qiime_config
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/scripts/qiime_config (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/scripts/qiime_config 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,19 @@
+# qiime_config
+# WARNING: DO NOT EDIT OR DELETE Qiime/qiime_config
+# To overwrite defaults, copy this file to $HOME/.qiime_config or a full path
+# specified by $QIIME_CONFIG_FP and edit that copy of the file.
+
+cluster_jobs_fp
+python_exe_fp python
+working_dir .
+blastmat_dir /usr/share/ncbi/data
+blastall_fp blastall
+rdp_classifier_fp
+pynast_template_alignment_fp
+pynast_template_alignment_blastdb
+template_alignment_lanemask_fp
+jobs_to_start 1
+seconds_to_sleep 60
+qiime_scripts_dir /usr/lib/qiime/bin/
+temp_dir /tmp
+pyronoise_data_fp /usr/local/bioinf/denoiser/denoiser/Data/LookUp.dat
Added: trunk/packages/qiime/branches/lucid/debian/scripts/shell/.bashrc
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/scripts/shell/.bashrc (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/scripts/shell/.bashrc 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,12 @@
+# Startup script for BASH with Qiime environment.
+# Source the user's default environent.
+test -e "/etc/bash.bashrc" && source "/etc/bash.bashrc"
+test -e "~/.bashrc" && source "~/.bashrc"
+
+help()
+{
+ cat "$QIIME_HELP_TEXT"
+}
+
+source /usr/lib/qiime/shell/qiime_environment
+PS1="$PS1 qiime > "
Added: trunk/packages/qiime/branches/lucid/debian/scripts/shell/.zshrc
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/scripts/shell/.zshrc (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/scripts/shell/.zshrc 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,14 @@
+# Startup script for ZSH with Qiime environment.
+if [ -e "$ZOLDDOTDIR/.zshrc" ] ; then
+ source "$ZOLDDOTDIR/.zshrc"
+ unset ZOLDDOTDIR
+fi
+
+source /usr/lib/qiime/shell/qiime_environment
+
+help()
+{
+ cat "$QIIME_HELP_TEXT"
+}
+
+PROMPT="$PROMPT qiime > "
Added: trunk/packages/qiime/branches/lucid/debian/scripts/shell/qiime_environment
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/scripts/shell/qiime_environment (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/scripts/shell/qiime_environment 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,12 @@
+#In the /usr/lib/qiime/shell directory are .zshrc and .bashrc files to set up the environment
+#needed for running Qiime. There may be a less hacky way of doing this but it works for now.
+
+# Qiime basic environment. Note that sourcing this file multiple times is not idempotent
+# and should be avoided!
+# This file needs to be readable by /bin/sh and zsh so no bash-isms allowed.
+
+export PYTHONPATH=$PYTHONPATH/:/usr/share/pyshared/qiime
+export PATH=$PATH:/usr/lib/qiime/bin
+export QIIME_CONFIG_FP=/etc/qiime/qiime_config
+export BLASTMAT=/usr/share/ncbi/data
+export QIIME_HELP_TEXT=/usr/lib/qiime/shell/qiime_help
Added: trunk/packages/qiime/branches/lucid/debian/scripts/shell/qiime_help
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/scripts/shell/qiime_help (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/scripts/shell/qiime_help 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,47 @@
+This is a proto-manpage for Qiime on Debian/Bio-Linux.
+Some of this info alternatively belongs in README.Debian.
+
+INVOCATION:
+
+ To run a Qiime command such as check_id_map.py:
+
+ % qiime check_id_map [...]
+
+ or just type 'qiime' to get a shell environment where all Qiime commands are available, ie:
+
+ % 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/
Added: trunk/packages/qiime/branches/lucid/debian/scripts/uclust
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/scripts/uclust (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/scripts/uclust 2011-08-29 09:02:22 UTC (rev 7575)
@@ -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
+"""
Added: trunk/packages/qiime/branches/lucid/debian/source/format
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/source/format (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/source/format 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/qiime/branches/lucid/debian/watch
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/watch (rev 0)
+++ trunk/packages/qiime/branches/lucid/debian/watch 2011-08-29 09:02:22 UTC (rev 7575)
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/qiime/Qiime-([.0-9]+)\.tar\.gz
More information about the debian-med-commit
mailing list