Author: tbooth-guest Date: 2011-11-04 12:29:51 +0000 (Fri, 04 Nov 2011) New Revision: 8407
Modified: trunk/packages/qiime/branches/lucid/debian/changelog trunk/packages/qiime/branches/lucid/debian/control trunk/packages/qiime/branches/lucid/debian/patches/series trunk/packages/qiime/branches/lucid/debian/rules trunk/packages/qiime/branches/lucid/debian/scripts/qiime_config trunk/packages/qiime/branches/lucid/debian/scripts/shell/qiime_environment trunk/packages/qiime/branches/lucid/debian/scripts/uclust Log: Some small fixes to Qiime including environment settings to pick up helper tools. Everything apart from the changelog and rules file should probably be pushed to the Debian package too. Modified: trunk/packages/qiime/branches/lucid/debian/changelog =================================================================== --- trunk/packages/qiime/branches/lucid/debian/changelog 2011-11-04 04:05:17 UTC (rev 8406) +++ trunk/packages/qiime/branches/lucid/debian/changelog 2011-11-04 12:29:51 UTC (rev 8407) @@ -1,10 +1,9 @@ -qiime (1.3.0-1) unstable; urgency=low +qiime (1.3.0-0ubuntu6) lucid; urgency=low - * Bringing qiime to Debian - [Steffen] - * Some reformatting of debian/control + * Attempt to fix some errors reported by print_qiime_config -t + Fixes to environment, configuration and small patches - -- Tim Booth <[email protected]> Fri, 26 Aug 2011 17:48:30 +0200 + -- Tim Booth <[email protected]> Wed, 02 Nov 2011 18:06:37 +0000 qiime (1.3.0-0ubuntu5) lucid; urgency=low Modified: trunk/packages/qiime/branches/lucid/debian/control =================================================================== --- trunk/packages/qiime/branches/lucid/debian/control 2011-11-04 04:05:17 UTC (rev 8406) +++ trunk/packages/qiime/branches/lucid/debian/control 2011-11-04 12:29:51 UTC (rev 8407) @@ -5,7 +5,7 @@ Uploaders: Steffen Moeller <[email protected]>, Tim Booth <[email protected]> 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/ +Homepage: http://www.qiime.org/ 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 Modified: trunk/packages/qiime/branches/lucid/debian/patches/series =================================================================== --- trunk/packages/qiime/branches/lucid/debian/patches/series 2011-11-04 04:05:17 UTC (rev 8406) +++ trunk/packages/qiime/branches/lucid/debian/patches/series 2011-11-04 12:29:51 UTC (rev 8407) @@ -1,2 +1,3 @@ python26_trim_sff_primers.patch fix_shebang_lines.patch +fix_binary_helper_location.patch Modified: trunk/packages/qiime/branches/lucid/debian/rules =================================================================== --- trunk/packages/qiime/branches/lucid/debian/rules 2011-11-04 04:05:17 UTC (rev 8406) +++ trunk/packages/qiime/branches/lucid/debian/rules 2011-11-04 12:29:51 UTC (rev 8407) @@ -27,7 +27,7 @@ # 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 +# Default configuration goes into /etc/qiime/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:: @@ -47,3 +47,4 @@ ( 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 $(ROOTDIR)/usr/qiime + Modified: trunk/packages/qiime/branches/lucid/debian/scripts/qiime_config =================================================================== --- trunk/packages/qiime/branches/lucid/debian/scripts/qiime_config 2011-11-04 04:05:17 UTC (rev 8406) +++ trunk/packages/qiime/branches/lucid/debian/scripts/qiime_config 2011-11-04 12:29:51 UTC (rev 8407) @@ -8,7 +8,6 @@ working_dir . blastmat_dir /usr/share/ncbi/data blastall_fp blastall -rdp_classifier_fp pynast_template_alignment_fp pynast_template_alignment_blastdb template_alignment_lanemask_fp @@ -16,4 +15,3 @@ seconds_to_sleep 60 qiime_scripts_dir /usr/lib/qiime/bin/ temp_dir /tmp -pyronoise_data_fp /usr/local/bioinf/denoiser/denoiser/Data/LookUp.dat Modified: trunk/packages/qiime/branches/lucid/debian/scripts/shell/qiime_environment =================================================================== --- trunk/packages/qiime/branches/lucid/debian/scripts/shell/qiime_environment 2011-11-04 04:05:17 UTC (rev 8406) +++ trunk/packages/qiime/branches/lucid/debian/scripts/shell/qiime_environment 2011-11-04 12:29:51 UTC (rev 8407) @@ -6,7 +6,11 @@ # This file needs to be readable by /bin/sh and zsh so no bash-isms allowed. export PYTHONPATH=$PYTHONPATH/:/usr/share/pyshared/qiime -export PATH=$PATH:/usr/lib/qiime/bin -export QIIME_CONFIG_FP=/etc/qiime/qiime_config -export BLASTMAT=/usr/share/ncbi/data +export PATH="$PATH:/usr/lib/qiime/bin:/usr/share/ampliconnoise/Scripts:/usr/lib/ChimeraSlayer" export QIIME_HELP_TEXT=/usr/lib/qiime/shell/qiime_help +export QIIME_CONFIG_FP=${QIIME_CONFIG_FP:-/etc/qiime/qiime_config} +export BLASTMAT=${BLASTMAT:-/usr/share/ncbi/data} + +# Mike Cox reports these are wanted for Ampliconnoise +export PYRO_LOOKUP_FILE=${PYRO_LOOKUP_FILE:-/usr/share/ampliconnoise/Data/LookUp_E123.dat} +export SEQ_LOOKUP_FILE=${SEQ_LOOKUP_FILE:-/usr/share/ampliconnoise/Data/Tran.dat} Modified: trunk/packages/qiime/branches/lucid/debian/scripts/uclust =================================================================== --- trunk/packages/qiime/branches/lucid/debian/scripts/uclust 2011-11-04 04:05:17 UTC (rev 8406) +++ trunk/packages/qiime/branches/lucid/debian/scripts/uclust 2011-11-04 12:29:51 UTC (rev 8407) @@ -24,7 +24,7 @@ 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 + http://www.drive5.com/uclust/downloads1_2_22q.html Download the $bits binary, then: sudo cp uclustq1.2.21_* /usr/local/bin/uclust _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
