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 <[email protected]> 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 <[email protected]> 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/ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
