[med-svn] r19784 - in trunk/packages/qiime/trunk/debian: . scripts
Timothy Booth
tbooth-guest at moszumanska.debian.org
Thu Jul 30 13:52:31 UTC 2015
Author: tbooth-guest
Date: 2015-07-30 13:52:31 +0000 (Thu, 30 Jul 2015)
New Revision: 19784
Added:
trunk/packages/qiime/trunk/debian/qiime.1.ronn
trunk/packages/qiime/trunk/debian/qiime.manpages
trunk/packages/qiime/trunk/debian/qiime_config
trunk/packages/qiime/trunk/debian/scripts/print_qiime_config_all
Removed:
trunk/packages/qiime/trunk/debian/qiime.links
Modified:
trunk/packages/qiime/trunk/debian/changelog
trunk/packages/qiime/trunk/debian/control
trunk/packages/qiime/trunk/debian/rules
Log:
This completes the sync between Bio-Linux and Debian.
Note that the build for QIIME 1.9.1 is not yet tested. Await the next
commit before actually attempting to use this package or trying to push
in your own fixes.
Modified: trunk/packages/qiime/trunk/debian/changelog
===================================================================
--- trunk/packages/qiime/trunk/debian/changelog 2015-07-30 11:27:10 UTC (rev 19783)
+++ trunk/packages/qiime/trunk/debian/changelog 2015-07-30 13:52:31 UTC (rev 19784)
@@ -1,3 +1,13 @@
+qiime (1.9.1+dfsg-1ubuntu1) trusty; urgency=medium
+
+ * New upstream - should be a bugfix upgrade
+ * Attempt to re-sync Bio-Linux and Deb Med packages
+ * Ensure we depend on biom-format version
+ * Add in manpages and print_qiime_config_all helper script
+ * Remove link to king which is no longer used
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Thu, 30 Jul 2015 10:17:08 +0100
+
qiime (1.9.0+dfsg-1) UNRELEASED; urgency=medium
* Take over changes from BioLinux for new upstream version
Modified: trunk/packages/qiime/trunk/debian/control
===================================================================
--- trunk/packages/qiime/trunk/debian/control 2015-07-30 11:27:10 UTC (rev 19783)
+++ trunk/packages/qiime/trunk/debian/control 2015-07-30 13:52:31 UTC (rev 19784)
@@ -29,7 +29,7 @@
pynast (>= 1.2.2),
python-burrito (>= 0.9.0),
python-burrito-fillings (>= 0.1.0),
- python-biom-format,
+ python-biom-format (>= 2.1),
python-cogent (>= 1.5.3),
python-matplotlib,
python-mpi4py,
@@ -60,7 +60,7 @@
sortmerna,
sumatra,
swarm,
- vsearch
+ vsearch (>= 1.1.1)
Recommends: mothur,
rtax
Suggests: t-coffee,
Added: trunk/packages/qiime/trunk/debian/qiime.1.ronn
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.1.ronn (rev 0)
+++ trunk/packages/qiime/trunk/debian/qiime.1.ronn 2015-07-30 13:52:31 UTC (rev 19784)
@@ -0,0 +1,73 @@
+qiime(1) -- Quantitative Insights Into Microbial Ecology
+
+This is a short manpage for QIIME on Debian/Bio-Linux.
+You should refer to the main QIIME documentation at
+/usr/share/doc/qiime/html/index.html and also the QIIME section of the
+Bio-Linux tutorial at http://environmentalomics.org/bio-linux-training/.
+
+## INVOCATION:
+
+To run any QIIME command such as "validate_mapping_file.py":
+
+ _$_ `qiime` validate_mapping_file [...]
+
+or just type 'qiime' to get a customised shell environment where all QIIME commands
+are available exactly as documented, ie:
+
+ _$_ `qiime`
+
+ _$ qiime >_ `validate_mapping_file.py` [...]
+
+## PARAMETERS FILE:
+
+For certain QIIME commands, you are asked to indicate where your QIIME
+parameters file is. You can find an example file in the location
+/usr/share/doc/qiime/qiime_parameters_example.txt but the recommendation
+as of QIIME 1.7.0 is to only set values that you want to override and to
+let QIIME pick defaults for the others.
+
+## QIIME CONFIGURATION:
+
+QIIME reads configuration information from the file specified by
+**$QIIME_CONFIG_FP** or by default from **/etc/qiime/qiime_config**.
+It is unlikely you will need to change the settings in this file,
+but if you do you should copy it as **.qiime_config** in your home directory.
+
+## GREENGENES DATA:
+
+The qiime-data package now provides copies of the Greengenes core alignment
+template plus the lanemask file in **/usr/share/qiime/data** but you still need
+to download some extra data to use QIIME properly. Taxonomic databases are
+being updated all the time and you need to be sure which version you are
+using. See the QIIME main docs for more info on what you need.
+
+## PROGRAMS INVOKED BY QIIME:
+
+QIIME calls many applications and libraries in the course of performing an
+analysis. For consistency, it is important to know what versions were installed
+at the time of the analysis. To obtain a complete report type
+
+ `print_qiime_config_all`
+
+**NB:** The official release of QIIME stipulates very particular versions of all these
+programs in order to guarantee consistent results. This version of QIIME uses updated
+versions that are packages in the Debian software repository. If you want to obtain ressults
+consistent with the official QIIME pipeline then you need to install QIIME as set out on
+the main website.
+
+## UCLUST and USEARCH:
+
+You may install these manually if you want to use them, but as of QIIME 1.9
+all features should be available via the free SumaClust and vSearch programs.
+uClust and uSearch are not free software and come with usage restrictions
+for non-paying users.
+
+For more info, try running 'uclust' or 'usearch' at the QIIME prompt.
+
+## For more information about QIIME, please visit the home page at:
+
+ http://qiime.org
+
+## QIIME was packaged as part of the Bio-Linux project.
+
+ http://environmentalomics.org/bio-linux
Deleted: trunk/packages/qiime/trunk/debian/qiime.links
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.links 2015-07-30 11:27:10 UTC (rev 19783)
+++ trunk/packages/qiime/trunk/debian/qiime.links 2015-07-30 13:52:31 UTC (rev 19784)
@@ -1 +0,0 @@
-usr/share/java/king.jar usr/lib/qiime/support_files/jar/king.jar
Added: trunk/packages/qiime/trunk/debian/qiime.manpages
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.manpages (rev 0)
+++ trunk/packages/qiime/trunk/debian/qiime.manpages 2015-07-30 13:52:31 UTC (rev 19784)
@@ -0,0 +1 @@
+debian/*.1
Added: trunk/packages/qiime/trunk/debian/qiime_config
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime_config (rev 0)
+++ trunk/packages/qiime/trunk/debian/qiime_config 2015-07-30 13:52:31 UTC (rev 19784)
@@ -0,0 +1,28 @@
+# qiime_config
+# WARNING: DO NOT EDIT OR DELETE /etc/qiime/qiime_config
+# To overwrite defaults, copy this file to $HOME/.qiime_config or a path
+# specified by $QIIME_CONFIG_FP and edit that copy of the file.
+
+# This file refers to default GreenGenes data files installed by the qiime-data
+# package.
+
+cluster_jobs_fp
+python_exe_fp python
+working_dir .
+blastmat_dir /usr/share/ncbi/data
+blastall_fp blastall
+pynast_template_alignment_fp /usr/share/qiime/data/core_set_aligned.fasta.imputed
+#template_alignment_lanemask_fp /usr/share/qiime/data/lanemask_in_1s_and_0s
+pynast_template_alignment_blastdb
+jobs_to_start 1
+seconds_to_sleep 60
+qiime_scripts_dir /usr/lib/qiime/bin/
+temp_dir /tmp
+
+# Uncomment these to enable always re-training the RDP classifier, which is the
+# default behaviour for QIIME 1.9. This takes a lot of time and RAM, so
+# for Bio-Linux the default behaviour is to quickly use the built-in index.
+# If you are using another assignment method you may need to specify these settings
+# in all cases.
+assign_taxonomy_id_to_taxonomy_fp # /usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
+assign_taxonomy_reference_seqs_fp # /usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta
Modified: trunk/packages/qiime/trunk/debian/rules
===================================================================
--- trunk/packages/qiime/trunk/debian/rules 2015-07-30 11:27:10 UTC (rev 19783)
+++ trunk/packages/qiime/trunk/debian/rules 2015-07-30 13:52:31 UTC (rev 19784)
@@ -66,7 +66,7 @@
for path in denoiser/Data css images R js ; do \
dh_link -pqiime /usr/share/qiime/support_files/"$$path" /usr/lib/qiime/support_files/"$$path" ;\
done
- #Embed the Debian revision into the version
+ #Embed the Debian revision into the version which users see.
( v=$$(dpkg-parsechangelog | sed -n 's/^Version: \(.*\)/\1/p') ; \
cd debian/qiime ; \
f=usr/lib/qiime/bin/print_qiime_config.py ; \
Added: trunk/packages/qiime/trunk/debian/scripts/print_qiime_config_all
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/print_qiime_config_all (rev 0)
+++ trunk/packages/qiime/trunk/debian/scripts/print_qiime_config_all 2015-07-30 13:52:31 UTC (rev 19784)
@@ -0,0 +1,18 @@
+#!/bin/sh
+
+print_qiime_config.py -t
+
+echo
+
+echo "Here are the versions of the packages that QIIME depends on as reported by"
+echo "the system package manager:"
+echo
+
+dpkg -s qiime | perl -ne '/^Depends: (.*)/ &&
+ map {s/[ :].*//;
+ printf "%-26s: %s", $_, `dpkg -s "$_" | sed -n "/Version:/s/.* //p"`
+ }
+ grep {! /^lib/}
+ sort
+ split(/, /,"$1, mothur")' | uniq \
+&& { echo ; echo OK ; }
Property changes on: trunk/packages/qiime/trunk/debian/scripts/print_qiime_config_all
___________________________________________________________________
Added: svn:executable
+ *
More information about the debian-med-commit
mailing list