[med-svn] r6377 - in trunk/packages/qiime/trunk/debian: . scripts scripts/shell
Timothy Booth
tbooth-guest at alioth.debian.org
Thu Mar 24 14:46:41 UTC 2011
Author: tbooth-guest
Date: 2011-03-24 14:46:38 +0000 (Thu, 24 Mar 2011)
New Revision: 6377
Added:
trunk/packages/qiime/trunk/debian/conffiles
trunk/packages/qiime/trunk/debian/qiime.docs
trunk/packages/qiime/trunk/debian/scripts/
trunk/packages/qiime/trunk/debian/scripts/qiime
trunk/packages/qiime/trunk/debian/scripts/qiime_config
trunk/packages/qiime/trunk/debian/scripts/shell/
trunk/packages/qiime/trunk/debian/scripts/shell/.bashrc
trunk/packages/qiime/trunk/debian/scripts/shell/.zshrc
trunk/packages/qiime/trunk/debian/scripts/shell/qiime_environment
trunk/packages/qiime/trunk/debian/scripts/shell/qiime_help
Removed:
trunk/packages/qiime/trunk/debian/docs
Modified:
trunk/packages/qiime/trunk/debian/README.Debian
trunk/packages/qiime/trunk/debian/changelog
trunk/packages/qiime/trunk/debian/control
trunk/packages/qiime/trunk/debian/rules
Log:
Qiime is a work in progress. This package will build, but it
won't work right now.
Also, there are mentions of Bio-Linux packages which I had to put in to get it working
properly for my Bio-Linux testers. Hopefully these will be cleaned out long before
Qiime becomes a candidate for Debian.
Modified: trunk/packages/qiime/trunk/debian/README.Debian
===================================================================
--- trunk/packages/qiime/trunk/debian/README.Debian 2011-03-23 23:01:13 UTC (rev 6376)
+++ trunk/packages/qiime/trunk/debian/README.Debian 2011-03-24 14:46:38 UTC (rev 6377)
@@ -1,3 +1,9 @@
+Quick Start
+===========
+
+Type 'qiime' at the shell prompt before running any of the standard qiime
+commands.
+
QIIME for Debian
================
@@ -7,6 +13,10 @@
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 - efforts
+are underway by the Bio-Linux devlopers to port this work into Debian.
+
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
Modified: trunk/packages/qiime/trunk/debian/changelog
===================================================================
--- trunk/packages/qiime/trunk/debian/changelog 2011-03-23 23:01:13 UTC (rev 6376)
+++ trunk/packages/qiime/trunk/debian/changelog 2011-03-24 14:46:38 UTC (rev 6377)
@@ -1,3 +1,20 @@
+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)
Modified: trunk/packages/qiime/trunk/debian/control
===================================================================
--- trunk/packages/qiime/trunk/debian/control 2011-03-23 23:01:13 UTC (rev 6376)
+++ trunk/packages/qiime/trunk/debian/control 2011-03-24 14:46:38 UTC (rev 6377)
@@ -12,9 +12,10 @@
Package: qiime
Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}
-Recommends: blast2
-Suggests: muscle, infernal, t-coffee
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}, python-pynast
+Recommends: blast2, cd-hit, denoiser, rdp-classifier, chimeraslayer, muscle, infernal, fasttree
+Suggests: t-coffee, cytoscape
+Conflicts: bio-linux-qiime (<= bl1.1.x)
XB-Python-Version: ${python:Versions}
Description: Quantitative Insights Into Microbial Ecology
QIIME (canonically pronounced ‘Chime’) is a pipeline for performing
Deleted: trunk/packages/qiime/trunk/debian/docs
===================================================================
--- trunk/packages/qiime/trunk/debian/docs 2011-03-23 23:01:13 UTC (rev 6376)
+++ trunk/packages/qiime/trunk/debian/docs 2011-03-24 14:46:38 UTC (rev 6377)
@@ -1,5 +0,0 @@
-README
-ChangeLog
-qiime_parameters.txt
-qiime_tutorial/
-doc/*
Added: trunk/packages/qiime/trunk/debian/qiime.docs
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.docs (rev 0)
+++ trunk/packages/qiime/trunk/debian/qiime.docs 2011-03-24 14:46:38 UTC (rev 6377)
@@ -0,0 +1,6 @@
+README
+ChangeLog
+qiime_parameters.txt
+qiime_tutorial/
+doc/_build/*
+doc/vb_files
Modified: trunk/packages/qiime/trunk/debian/rules
===================================================================
--- trunk/packages/qiime/trunk/debian/rules 2011-03-23 23:01:13 UTC (rev 6376)
+++ trunk/packages/qiime/trunk/debian/rules 2011-03-24 14:46:38 UTC (rev 6377)
@@ -5,9 +5,30 @@
#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??
clean::
rm -rf doc/_build
+
+#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?
+common-binary-fixup-indep::
+ 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
+ cp -R --no-preserve=all debian/scripts/shell $(ROOTDIR)/usr/lib/qiime
+ 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
+ ( cd $(ROOTDIR)/usr/share/doc/`dh_listpackages` ; mv ChangeLog.gz changelog.gz || true )
Added: trunk/packages/qiime/trunk/debian/scripts/qiime
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/qiime (rev 0)
+++ trunk/packages/qiime/trunk/debian/scripts/qiime 2011-03-24 14:46:38 UTC (rev 6377)
@@ -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/trunk/debian/scripts/qiime_config
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/qiime_config (rev 0)
+++ trunk/packages/qiime/trunk/debian/scripts/qiime_config 2011-03-24 14:46:38 UTC (rev 6377)
@@ -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 $QIIME_CONFIG_FP and edit that copy of the file.
+
+cluster_jobs_fp
+python_exe_fp python
+working_dir .
+blastmat_dir /usr/share/ncbi/data
+blastall_fp blastall
+rdp_classifier_fp
+pynast_template_alignment_fp
+pynast_template_alignment_blastdb
+template_alignment_lanemask_fp
+jobs_to_start 1
+seconds_to_sleep 60
+qiime_scripts_dir /usr/lib/qiime/bin/
+temp_dir /tmp
+pyronoise_data_fp /usr/local/bioinf/denoiser/denoiser/Data/LookUp.dat
Added: trunk/packages/qiime/trunk/debian/scripts/shell/.bashrc
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/shell/.bashrc (rev 0)
+++ trunk/packages/qiime/trunk/debian/scripts/shell/.bashrc 2011-03-24 14:46:38 UTC (rev 6377)
@@ -0,0 +1,12 @@
+# Startup script for BASH with Qiime environment.
+# Source the user's default environent.
+test -e "/etc/bash.bashrc" && source "/etc/bash.bashrc"
+test -e "~/.bashrc" && source "~/.bashrc"
+
+help()
+{
+ cat "$QIIME_HELP_TEXT"
+}
+
+source /usr/lib/qiime/shell/qiime_environment
+PS1="$PS1 qiime > "
Added: trunk/packages/qiime/trunk/debian/scripts/shell/.zshrc
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/shell/.zshrc (rev 0)
+++ trunk/packages/qiime/trunk/debian/scripts/shell/.zshrc 2011-03-24 14:46:38 UTC (rev 6377)
@@ -0,0 +1,14 @@
+# Startup script for ZSH with Qiime environment.
+if [ -e "$ZOLDDOTDIR/.zshrc" ] ; then
+ source "$ZOLDDOTDIR/.zshrc"
+ unset ZOLDDOTDIR
+fi
+
+source /usr/lib/qiime/shell/qiime_environment
+
+help()
+{
+ cat "$QIIME_HELP_TEXT"
+}
+
+PROMPT="$PROMPT qiime > "
Added: trunk/packages/qiime/trunk/debian/scripts/shell/qiime_environment
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/shell/qiime_environment (rev 0)
+++ trunk/packages/qiime/trunk/debian/scripts/shell/qiime_environment 2011-03-24 14:46:38 UTC (rev 6377)
@@ -0,0 +1,12 @@
+#In the /usr/lib/qiime/shell directory are .zshrc and .bashrc files to set up the environment
+#needed for running Qiime. There may be a less hacky way of doing this but it works for now.
+
+# Qiime basic environment. Note that sourcing this file multiple times is not idempotent
+# and should be avoided!
+# This file needt to be readable by /bin/sh so no bash-isms allowed.
+
+export PYTHONPATH=$PYTHONPATH/:/usr/share/pyshared/qiime:/usr/local/bioinf/denoiser/denoiser
+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/trunk/debian/scripts/shell/qiime_help
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/shell/qiime_help (rev 0)
+++ trunk/packages/qiime/trunk/debian/scripts/shell/qiime_help 2011-03-24 14:46:38 UTC (rev 6377)
@@ -0,0 +1,16 @@
+This is the old help text - file locations are wrong - needs re-writing...
+
+Welcome to Qiime on Bio-Linux.
+You can now type any of the qiime commands at the qiime prompt.
+
+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.
+
+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.
+
+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.
+
+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.
+
+For more information about Qiime, please refer to the Qiime documentation at:
+
+http://qiime.sourceforge.net/
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