[med-svn] r16413 - in trunk/packages/qiime/trunk/debian: . patches scripts scripts/shell
Timothy Booth
tbooth-guest at moszumanska.debian.org
Mon Mar 10 14:53:55 UTC 2014
Author: tbooth-guest
Date: 2014-03-10 14:53:55 +0000 (Mon, 10 Mar 2014)
New Revision: 16413
Added:
trunk/packages/qiime/trunk/debian/patches/detect_matplotlib_version
trunk/packages/qiime/trunk/debian/patches/fix_script_usage_tests
trunk/packages/qiime/trunk/debian/patches/prevent_download_on_builds.patch
trunk/packages/qiime/trunk/debian/patches/relax_mothur_blast_raxml_versions
trunk/packages/qiime/trunk/debian/qiime-data.install
trunk/packages/qiime/trunk/debian/scripts/FastTree
trunk/packages/qiime/trunk/debian/scripts/ParsInsert
trunk/packages/qiime/trunk/debian/scripts/make_emperor.py
Modified:
trunk/packages/qiime/trunk/debian/README.source
trunk/packages/qiime/trunk/debian/changelog
trunk/packages/qiime/trunk/debian/control
trunk/packages/qiime/trunk/debian/copyright
trunk/packages/qiime/trunk/debian/patches/check_config_file_in_new_location.patch
trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch
trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files
trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier
trunk/packages/qiime/trunk/debian/patches/series
trunk/packages/qiime/trunk/debian/qiime.README.Debian
trunk/packages/qiime/trunk/debian/qiime.install
trunk/packages/qiime/trunk/debian/qiime.links
trunk/packages/qiime/trunk/debian/rules
trunk/packages/qiime/trunk/debian/scripts/qiime
trunk/packages/qiime/trunk/debian/scripts/qiime_config
trunk/packages/qiime/trunk/debian/scripts/shell/qiime_help
Log:
QIIME 1.8.0 as put onto Bio-Linux
Modified: trunk/packages/qiime/trunk/debian/README.source
===================================================================
--- trunk/packages/qiime/trunk/debian/README.source 2014-03-10 13:33:48 UTC (rev 16412)
+++ trunk/packages/qiime/trunk/debian/README.source 2014-03-10 14:53:55 UTC (rev 16413)
@@ -15,7 +15,7 @@
New comments by Tim:
-I borrowed the Bio-Linux approach for Qiime which may or may not be the best idea.
+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
@@ -31,16 +31,29 @@
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
+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 install it.
+gracefully but it is still up to the user to fetch and install it.
Other dependencies/TODO:
------------------------
-Everything else needed should be packaged, if not in Debian proper then in the SVN.
+Everything else needed should be packaged, if not in Debian proper then in the SVN. QIIME
+keeps adding new deps so these need to be checked with each release.
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
+emperor and king are both troublesome in their own ways. We really need Emperor for 1.8.0+
+QIIME data
+----------
+
+The QIIME installation instructions say that you need to download some core files from Greengenes.
+Since these barely change and are included in the upstream tarball I am now putting them into the
+qiime-data package for easy access. I have noted in copyright that these are CC licensed.
+
+See here for a discussion of what these are and why they don't change:
+
+https://groups.google.com/forum/?hl=en-US#!searchin/qiime-forum/greengenes/qiime-forum/SvXFetaLNCM/HE6bsBY0yZIJ
+
Modified: trunk/packages/qiime/trunk/debian/changelog
===================================================================
--- trunk/packages/qiime/trunk/debian/changelog 2014-03-10 13:33:48 UTC (rev 16412)
+++ trunk/packages/qiime/trunk/debian/changelog 2014-03-10 14:53:55 UTC (rev 16413)
@@ -1,3 +1,25 @@
+qiime (1.8.0-1biolinux1) precise; urgency=low
+
+ * Make QIIME report the Debian version, because the patches we
+ add are significant.
+ * New dep on Emperor
+ * Add new deps on qcli and promote some recommends to dependencies
+ based on http://qiime.org/install/install.html#manually-installing-qiime
+ * Add little wrapper script to call parsinsert as ParsInsert
+ * Pulled the adsense patch from Andreas. Noted these packages are totally
+ out of sync. Oh well.
+ * Dropped biom 1108 patch as this is in upstream
+ * Added greengenes core data in /usr/share/qiime/data as this doesn't
+ ever seem to change and other QIIME distributions include it.
+ * Modified help text to reflect recent changes.
+ * Patch on unit tests to overcome some problems running them
+ * Remove denoiser symlink as there is no need for it now
+ * Prevent attempts to download stuff (uclust, fasttree) during build
+ * Added suggested dep on r-cran-optparse
+ * More determined cleanup of temporary test data
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Mon, 10 Mar 2014 14:20:08 +0000
+
qiime (1.8.0+dfsg-3) UNRELEASED; urgency=medium
TODO:
@@ -36,6 +58,13 @@
-- Andreas Tille <tille at debian.org> Sat, 21 Dec 2013 08:50:20 +0100
+qiime (1.7.0-0biolinux2) precise; urgency=low
+
+ * Added patch from https://github.com/qiime/qiime/pull/1108.patch
+ so we can/must use biom-format 1.2.0
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Wed, 29 Jan 2014 15:06:04 +0000
+
qiime (1.7.0+dfsg-1) unstable; urgency=low
* Upload preparations done for BioLinux to Debian
Modified: trunk/packages/qiime/trunk/debian/control
===================================================================
--- trunk/packages/qiime/trunk/debian/control 2014-03-10 13:33:48 UTC (rev 16412)
+++ trunk/packages/qiime/trunk/debian/control 2014-03-10 14:53:55 UTC (rev 16413)
@@ -23,22 +23,29 @@
Depends: ${shlibs:Depends},
${misc:Depends},
${python:Depends},
- pynast (>= 1.2),
+ pynast (>= 1.2.2),
python-cogent (>= 1.5.3),
+ emperor,
king | invue,
- python-biom-format,
- python-qcli
+ python-biom-format (>= 1.2.0),
+ fasttree,
+ python-qcli,
+ libjs-jquery,
+ python-matplotlib,
+ python-numpy,
+ libjs-jquery
+Pre-Depends: dpkg (>= 1.15.6~)
Recommends: blast2 | blast+-legacy,
cd-hit,
chimeraslayer,
muscle,
infernal,
- fasttree,
ampliconnoise,
- python-matplotlib,
- python-numpy,
+ parsinsert,
+ clearcut,
+ qiime-data,
python-mpi4py,
- libjs-jquery
+ r-cran-optparse
Suggests: t-coffee,
cytoscape,
rdp-classifier,
@@ -87,6 +94,7 @@
Depends: ${misc:Depends},
libjs-jquery,
libjs-underscore
+Pre-Depends: dpkg (>= 1.15.6~)
Description: Quantitative Insights Into Microbial Ecology (tutorial)
QIIME (canonically pronounced ‘Chime’) is a pipeline for performing
microbial community analysis that integrates many third party tools which
@@ -123,3 +131,13 @@
modular to facilitate custom analyses.
.
This package contains the documentation and a tutorial.
+
+Package: qiime-data
+Section: science
+Architecture: all
+Depends: ${misc:Depends}
+Pre-Depends: dpkg (>= 1.15.6~)
+Description: Quantitative Insights Into Microbial Ecology (supporting data)
+ This package contains the GreenGenes core data set needed by QIIME for PyNAST
+ alignment and filtering, but you will still need to download the appropriate
+ database for taxonomic assignment.
Modified: trunk/packages/qiime/trunk/debian/copyright
===================================================================
--- trunk/packages/qiime/trunk/debian/copyright 2014-03-10 13:33:48 UTC (rev 16412)
+++ trunk/packages/qiime/trunk/debian/copyright 2014-03-10 14:53:55 UTC (rev 16413)
@@ -29,6 +29,19 @@
On a Debian system, the GNU GPL license version 2 is distributed in the file
./usr/share/common-licenses/GPL-2..
+Files: qiime_test_data/align_seqs/core_set_aligned.fasta.imputed
+ qiime_test_data/filter_alignment/lanemask_in_1s_and_0s
+Copyright: (C) The Greengenes Database Consortium <http://greengenes.secondgenome.com/>
+License: CC-BY-SA
+ The Greengenes Database by The Greengenes Database Consortium is licensed under
+ a Creative Commons Attribution-ShareAlike 3.0 Unported License.
+
+ Academic users should cite:
+ DeSantis, T. Z., P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller,
+ T. Huber, D. Dalevi, P. Hu, and G. L. Andersen. 2006.
+ Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible
+ with ARB. Appl Environ Microbiol 72:5069-72.
+
Files: debian/*
Copyright: 2010 Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>
Steffen Moeller <moeller at debian.org>
Modified: trunk/packages/qiime/trunk/debian/patches/check_config_file_in_new_location.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/check_config_file_in_new_location.patch 2014-03-10 13:33:48 UTC (rev 16412)
+++ trunk/packages/qiime/trunk/debian/patches/check_config_file_in_new_location.patch 2014-03-10 14:53:55 UTC (rev 16413)
@@ -3,7 +3,7 @@
--- a/scripts/print_qiime_config.py
+++ b/scripts/print_qiime_config.py
-@@ -210,8 +210,7 @@ class QIIMEConfig(TestCase):
+@@ -210,8 +210,7 @@
"""local qiime_config has no extra params"""
qiime_project_dir = get_qiime_project_dir()
Added: trunk/packages/qiime/trunk/debian/patches/detect_matplotlib_version
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/detect_matplotlib_version (rev 0)
+++ trunk/packages/qiime/trunk/debian/patches/detect_matplotlib_version 2014-03-10 14:53:55 UTC (rev 16413)
@@ -0,0 +1,11 @@
+--- a/scripts/print_qiime_config.py
++++ b/scripts/print_qiime_config.py
+@@ -306,7 +306,7 @@
+ max_acceptable_version = (1,3,1)
+ try:
+ from matplotlib import __version__ as matplotlib_lib_version
+- version = tuple(map(int,matplotlib_lib_version.split('.')))
++ version = tuple(map(lambda x: int(x.replace("rc","")),matplotlib_lib_version.split('.')))
+ pass_test = (version >= min_acceptable_version and
+ version <= max_acceptable_version)
+ version_string = str(matplotlib_lib_version)
Modified: trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch 2014-03-10 13:33:48 UTC (rev 16412)
+++ trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch 2014-03-10 14:53:55 UTC (rev 16413)
@@ -1,6 +1,6 @@
--- a/qiime/denoiser/utils.py
+++ b/qiime/denoiser/utils.py
-@@ -60,8 +60,9 @@ def get_denoiser_data_dir():
+@@ -60,8 +60,9 @@
def get_flowgram_ali_exe():
"""Return the path to the flowgram alignment prog
"""
Modified: trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files 2014-03-10 13:33:48 UTC (rev 16412)
+++ trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files 2014-03-10 14:53:55 UTC (rev 16413)
@@ -4,7 +4,7 @@
--- a/qiime/util.py
+++ b/qiime/util.py
-@@ -302,8 +302,9 @@ def get_qiime_project_dir():
+@@ -302,8 +302,9 @@
# Get the directory containing util.py
current_dir_path = dirname(current_file_path)
# Return the directory containing the directory containing util.py
Added: trunk/packages/qiime/trunk/debian/patches/fix_script_usage_tests
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_script_usage_tests (rev 0)
+++ trunk/packages/qiime/trunk/debian/patches/fix_script_usage_tests 2014-03-10 14:53:55 UTC (rev 16413)
@@ -0,0 +1,34 @@
+--- a/qiime/test.py
++++ b/qiime/test.py
+@@ -14,7 +14,7 @@
+ from os import chdir, getcwd
+ from shutil import copytree, rmtree
+ from glob import glob
+-from site import addsitedir
++import sys
+ from tempfile import NamedTemporaryFile
+ from cogent.util.misc import remove_files
+ from qcli.test import (TimeExceededError,
+@@ -669,7 +669,9 @@
+ if verbose:
+ print 'Tests to run:\n %s' % ' '.join(tests)
+
+- addsitedir(scripts_dir)
++ #addsitedir(scripts_dir)
++ # This is not strong enough. The scripts-dir must be the first thing in the PATH
++ sys.path = [ scripts_dir ] + sys.path
+
+ failed_tests = []
+ warnings = []
+--- a/tests/all_tests.py
++++ b/tests/all_tests.py
+@@ -94,6 +94,9 @@
+ bad_tests.append(unittest_name)
+
+ qiime_test_data_dir = join(get_qiime_project_dir(),'qiime_test_data')
++ #Allow tests to be run without installing test data to system dir
++ if exists("../qiime_test_data"):
++ qiime_test_data_dir = "../qiime_test_data"
+ qiime_test_data_dir_exists = exists(qiime_test_data_dir)
+ if not opts.suppress_script_usage_tests and qiime_test_data_dir_exists:
+ if opts.script_usage_tests != None:
Modified: trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier 2014-03-10 13:33:48 UTC (rev 16412)
+++ trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier 2014-03-10 14:53:55 UTC (rev 16413)
@@ -4,7 +4,7 @@
This is a nasty hack and hopefully the patch can be dropped for QIIME 1.6
--- a/qiime/assign_taxonomy.py
+++ b/qiime/assign_taxonomy.py
-@@ -65,14 +65,20 @@ def validate_rdp_version(rdp_jarpath=Non
+@@ -65,14 +65,20 @@
"http://qiime.org/install/install.html#rdp-install"
)
@@ -34,7 +34,7 @@
"RDP Classifier does not look like version 2.2 or greater."
--- a/scripts/assign_taxonomy.py
+++ b/scripts/assign_taxonomy.py
-@@ -301,6 +301,11 @@ def main():
+@@ -301,6 +301,11 @@
params['training_data_properties_fp'] = opts.training_data_properties_fp
params['max_memory'] = "%sM" % opts.rdp_max_memory
Added: trunk/packages/qiime/trunk/debian/patches/prevent_download_on_builds.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/prevent_download_on_builds.patch (rev 0)
+++ trunk/packages/qiime/trunk/debian/patches/prevent_download_on_builds.patch 2014-03-10 14:53:55 UTC (rev 16413)
@@ -0,0 +1,16 @@
+--- a/setup.py
++++ b/setup.py
+@@ -175,13 +175,6 @@
+ else:
+ print "GHC not installed, so cannot build the Denoiser binary."
+
+- if app_available('gcc'):
+- build_FastTree()
+- else:
+- print "GCC not installed, so cannot build FastTree"
+-
+- if download_UCLUST():
+- print "UCLUST could not be installed."
+
+ # taken from PyNAST
+ classes = """
Added: trunk/packages/qiime/trunk/debian/patches/relax_mothur_blast_raxml_versions
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/relax_mothur_blast_raxml_versions (rev 0)
+++ trunk/packages/qiime/trunk/debian/patches/relax_mothur_blast_raxml_versions 2014-03-10 14:53:55 UTC (rev 16413)
@@ -0,0 +1,29 @@
+--- a/scripts/print_qiime_config.py
++++ b/scripts/print_qiime_config.py
+@@ -467,7 +467,7 @@
+ version_string = stdout.strip().split(' ')[1].strip()
+ try:
+ version = tuple(map(int,version_string.split('.')))
+- pass_test = version == acceptable_version
++ pass_test = version >= acceptable_version
+ except ValueError:
+ pass_test = False
+ version_string = stdout
+@@ -556,7 +556,7 @@
+ version_string = stdout.strip().split(' ')[1].strip('v.')
+ try:
+ version = tuple(map(int,version_string.split('.')))
+- pass_test = version == acceptable_version
++ pass_test = version >= acceptable_version
+ except ValueError:
+ pass_test = False
+ version_string = stdout
+@@ -579,7 +579,7 @@
+
+ def test_raxmlHPC_supported_version(self):
+ """raxmlHPC is in path and version is supported """
+- acceptable_version = [(7,3,0),(7,3,0)]
++ acceptable_version = [(7,3,0),(7,3,5)]
+ self.assertTrue(app_path('raxmlHPC'),
+ "raxmlHPC not found. This may or may not be a problem depending on "+\
+ "which components of QIIME you plan to use.")
Modified: trunk/packages/qiime/trunk/debian/patches/series
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/series 2014-03-10 13:33:48 UTC (rev 16412)
+++ trunk/packages/qiime/trunk/debian/patches/series 2014-03-10 14:53:55 UTC (rev 16413)
@@ -2,5 +2,9 @@
fix_binary_helper_location.patch
make_qiime_accept_new_rdp_classifier
fix_path_for_support_files
+detect_matplotlib_version
+relax_mothur_blast_raxml_versions
prevent_google_addsense.patch
+fix_script_usage_tests
+prevent_download_on_builds.patch
exclude_tests_that_need_to_fail.patch
Added: trunk/packages/qiime/trunk/debian/qiime-data.install
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime-data.install (rev 0)
+++ trunk/packages/qiime/trunk/debian/qiime-data.install 2014-03-10 14:53:55 UTC (rev 16413)
@@ -0,0 +1,2 @@
+qiime_test_data/align_seqs/core_set_aligned.fasta.imputed /usr/share/qiime/data
+qiime_test_data/filter_alignment/lanemask_in_1s_and_0s /usr/share/qiime/data
Modified: trunk/packages/qiime/trunk/debian/qiime.README.Debian
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.README.Debian 2014-03-10 13:33:48 UTC (rev 16412)
+++ trunk/packages/qiime/trunk/debian/qiime.README.Debian 2014-03-10 14:53:55 UTC (rev 16413)
@@ -28,7 +28,7 @@
The distribution is set to contrib because of
* the strong recommends to use uclust that is not shipped with
- Debian as a binary only package.
+ Debian as a binary only package with a restrictive license.
Disambiguation of versions in bio-linux, Debian and Ubuntu
Modified: trunk/packages/qiime/trunk/debian/qiime.install
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.install 2014-03-10 13:33:48 UTC (rev 16412)
+++ trunk/packages/qiime/trunk/debian/qiime.install 2014-03-10 14:53:55 UTC (rev 16413)
@@ -4,6 +4,9 @@
debian/scripts/qiime_config etc/qiime
debian/scripts/uclust usr/lib/qiime/bin
debian/scripts/usearch* usr/lib/qiime/bin
+debian/scripts/ParsInsert usr/lib/qiime/bin
+debian/scripts/FastTree usr/lib/qiime/bin
+debian/scripts/*.py usr/lib/qiime/bin
debian/tmp/usr/bin/*.py usr/lib/qiime/bin
qiime/support_files/denoiser/FlowgramAlignment/FlowgramAli_4frame usr/lib/qiime/support_files/denoiser/bin
qiime/*.py usr/share/pyshared/qiime
Modified: trunk/packages/qiime/trunk/debian/qiime.links
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.links 2014-03-10 13:33:48 UTC (rev 16412)
+++ trunk/packages/qiime/trunk/debian/qiime.links 2014-03-10 14:53:55 UTC (rev 16413)
@@ -1,8 +1,6 @@
-usr/bin/qiime usr/bin/denoiser
usr/share/java/king.jar usr/lib/qiime/support_files/jar/king.jar
# Needed because QIIME wants to call the BIOM format tools this way
-usr/bin/add_metadata usr/lib/qiime/bin/add_metadata.py
-# usr/bin/test_biom_validator usr/lib/qiime/bin/test_biom_validator.py
+usr/bin/add_biom_metadata usr/lib/qiime/bin/add_metadata.py
usr/bin/biom_validator usr/lib/qiime/bin/biom_validator.py
usr/bin/subset_biom usr/lib/qiime/bin/subset_biom.py
usr/bin/convert_biom usr/lib/qiime/bin/convert_biom.py
Modified: trunk/packages/qiime/trunk/debian/rules
===================================================================
--- trunk/packages/qiime/trunk/debian/rules 2014-03-10 13:33:48 UTC (rev 16412)
+++ trunk/packages/qiime/trunk/debian/rules 2014-03-10 14:53:55 UTC (rev 16413)
@@ -26,6 +26,7 @@
override_dh_auto_clean:
#Calling "python setup.py clean -a" actually triggers a
#rebuild, so don't do it.
+ rm -f *.logfile
rm -rf build
rm -rf doc/_build
( cd $(pkg)/support_files/denoiser/FlowgramAlignment && make clean ) || true
@@ -36,7 +37,7 @@
find qiime scripts -name '*.pyc' -delete
# Remove remainings from running the test suite
rm -f BLAST_temp_db*
- rm -rf jobs
+ rm -rf jobs tests/jobs
export ROOTDIR=debian/$(pkg)
@@ -60,6 +61,11 @@
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
+ ( v=$$(dpkg-parsechangelog | sed -n 's/^Version: \(.*\)/\1/p') ; \
+ cd debian/qiime ; \
+ f=usr/lib/qiime/bin/print_qiime_config.py ; \
+ sed -i 's/^\(__version__ = "\)1.*"/\1'$$v'"/' $$f )
override_dh_installchangelogs:
dh_installchangelogs ChangeLog.md
Added: trunk/packages/qiime/trunk/debian/scripts/FastTree
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/FastTree (rev 0)
+++ trunk/packages/qiime/trunk/debian/scripts/FastTree 2014-03-10 14:53:55 UTC (rev 16413)
@@ -0,0 +1,3 @@
+#!/bin/sh
+
+exec fasttree "$@"
Property changes on: trunk/packages/qiime/trunk/debian/scripts/FastTree
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/qiime/trunk/debian/scripts/ParsInsert
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/ParsInsert (rev 0)
+++ trunk/packages/qiime/trunk/debian/scripts/ParsInsert 2014-03-10 14:53:55 UTC (rev 16413)
@@ -0,0 +1,3 @@
+#!/bin/sh
+
+exec parsinsert "$@"
Property changes on: trunk/packages/qiime/trunk/debian/scripts/ParsInsert
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/qiime/trunk/debian/scripts/make_emperor.py
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/make_emperor.py (rev 0)
+++ trunk/packages/qiime/trunk/debian/scripts/make_emperor.py 2014-03-10 14:53:55 UTC (rev 16413)
@@ -0,0 +1,10 @@
+#!/usr/bin/python
+
+# The make_emperor command on Debian lacks a .py extension
+#exec make_emperor "$@"
+
+# But then if I use a standard shell wrapper I get complaints that the file
+# with a .py extension is not a Python file, so here's a Python equivalent.
+
+import os, sys
+os.execvp("make_emperor", ["make_emperor"] + sys.argv[1:])
Property changes on: trunk/packages/qiime/trunk/debian/scripts/make_emperor.py
___________________________________________________________________
Added: svn:executable
+ *
Modified: trunk/packages/qiime/trunk/debian/scripts/qiime
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/qiime 2014-03-10 13:33:48 UTC (rev 16412)
+++ trunk/packages/qiime/trunk/debian/scripts/qiime 2014-03-10 14:53:55 UTC (rev 16413)
@@ -21,7 +21,7 @@
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 "To start an interactive QIIME shell, you need to have 'bash' available and"
echo "in your path."
exit 1
fi
Modified: trunk/packages/qiime/trunk/debian/scripts/qiime_config
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/qiime_config 2014-03-10 13:33:48 UTC (rev 16412)
+++ trunk/packages/qiime/trunk/debian/scripts/qiime_config 2014-03-10 14:53:55 UTC (rev 16413)
@@ -1,17 +1,20 @@
# 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
+# 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
+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
-template_alignment_lanemask_fp
-jobs_to_start 1
-seconds_to_sleep 60
-qiime_scripts_dir /usr/lib/qiime/bin/
-temp_dir /tmp
+jobs_to_start 1
+seconds_to_sleep 60
+qiime_scripts_dir /usr/lib/qiime/bin/
+temp_dir /tmp
Modified: trunk/packages/qiime/trunk/debian/scripts/shell/qiime_help
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/shell/qiime_help 2014-03-10 13:33:48 UTC (rev 16412)
+++ trunk/packages/qiime/trunk/debian/scripts/shell/qiime_help 2014-03-10 14:53:55 UTC (rev 16413)
@@ -1,47 +1,50 @@
-This is a proto-manpage for Qiime on Debian/Bio-Linux.
-Some of this info alternatively belongs in README.Debian.
+This is a proto-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.
INVOCATION:
- To run a Qiime command such as check_id_map.py:
+ To run any QIIME command such as validate_mapping_file.py:
- % qiime check_id_map [...]
+ $ qiime validate_mapping_file [...]
- or just type 'qiime' to get a shell environment where all Qiime commands are available, ie:
+ or just type 'qiime' to get a shell environment where all QIIME commands
+ are available exactly as documented, ie:
- % qiime
- % qiime > check_id_map.py [...]
+ $ qiime
+ $ qiime > validate_mapping_file.py [...]
PARAMETERS FILE:
- 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/share/doc/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.
+ 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.
- 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.
-
GREENGENES DATA:
- 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.
+ 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.
QIIME CONFIGURATION:
- Qiime reads configuration information from the file specified by QIIME_CONFIG_FP.
- Your QIIME_CONFIG_FP is set to /etc/qiime/qiime_config. It is unlikely you will need to
- change the settings in this file.
+ 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.
-UCLUST:
+UCLUST and USEARCH:
- You may need to install UClust manually to use some Qiime functions.
- For more info, try running 'uclust' at the qiime prompt.
+ You may need to install these manually to use some QIIME functions.
+ These applications 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:
-For more information about Qiime, please refer to the Qiime documentation at:
-
- http://qiime.sourceforge.net/
+ http://qiime.org
More information about the debian-med-commit
mailing list