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 <[email protected]> Mon, 10 Mar 2014 14:20:08 +0000 + qiime (1.8.0+dfsg-3) UNRELEASED; urgency=medium TODO: @@ -36,6 +58,13 @@ -- Andreas Tille <[email protected]> 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 <[email protected]> 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 <[email protected]> Steffen Moeller <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
