Author: tbooth-guest Date: 2011-08-24 16:47:14 +0000 (Wed, 24 Aug 2011) New Revision: 7538
Added: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/patches/fix_shebang_lines.patch Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/README.source trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/changelog trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/rules trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/scripts/shell/qiime_environment Log: Updates and added commentary to README.source Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/README.source =================================================================== --- trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/README.source 2011-08-24 15:46:33 UTC (rev 7537) +++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/README.source 2011-08-24 16:47:14 UTC (rev 7538) @@ -1,9 +1,42 @@ QIIME for Debian - source ========================= +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 insatll it. + +Other dependencies/TODO: + +Everything else needed should be packaged, if not in Debian proper than 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 + + Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/changelog =================================================================== --- trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/changelog 2011-08-24 15:46:33 UTC (rev 7537) +++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/changelog 2011-08-24 16:47:14 UTC (rev 7538) @@ -1,3 +1,9 @@ +qiime (1.3.0-0ubuntu5) lucid; urgency=low + + * Very minor fix to scripts/shell/qiime_environment + + -- Tim Booth <[email protected]> Tue, 16 Aug 2011 12:35:06 +0100 + qiime (1.3.0-0ubuntu4) lucid; urgency=low * New upstream release. Needs newer Python-Cogent Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control =================================================================== --- trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control 2011-08-24 15:46:33 UTC (rev 7537) +++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/control 2011-08-24 16:47:14 UTC (rev 7538) @@ -13,7 +13,7 @@ Package: qiime Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}, python-pynast, python-cogent ( >= 1.5.1 ) -Recommends: blast2, cd-hit, rdp-classifier, chimeraslayer, muscle, infernal, fasttree, ampliconnoise +Recommends: blast2 | blast+-legacy, cd-hit, rdp-classifier, chimeraslayer, muscle, infernal, fasttree, ampliconnoise, python-matplotlib, python-numpy Conflicts: denoiser Replaces: denoiser Suggests: t-coffee, cytoscape Added: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/patches/fix_shebang_lines.patch =================================================================== --- trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/patches/fix_shebang_lines.patch (rev 0) +++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/patches/fix_shebang_lines.patch 2011-08-24 16:47:14 UTC (rev 7538) @@ -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" Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/rules =================================================================== --- trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/rules 2011-08-24 15:46:33 UTC (rev 7537) +++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/rules 2011-08-24 16:47:14 UTC (rev 7538) @@ -40,7 +40,8 @@ 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 - install -m 644 debian/scripts/qiime_config $(ROOTDIR)/etc/qiime/qiime_config + 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 $(ROOTDIR)/usr/share/doc/`dh_listpackages` ; mv ChangeLog.gz changelog.gz || true ) # And about the existence of /usr/qiime Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/scripts/shell/qiime_environment =================================================================== --- trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/scripts/shell/qiime_environment 2011-08-24 15:46:33 UTC (rev 7537) +++ trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/scripts/shell/qiime_environment 2011-08-24 16:47:14 UTC (rev 7538) @@ -3,9 +3,9 @@ # Qiime basic environment. Note that sourcing this file multiple times is not idempotent # and should be avoided! -# This file needt to be readable by /bin/sh so no bash-isms allowed. +# This file needs to be readable by /bin/sh and zsh so no bash-isms allowed. -export PYTHONPATH=$PYTHONPATH/:/usr/share/pyshared/qiime:/usr/local/bioinf/denoiser/denoiser +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
