[med-svn] r19739 - in trunk/packages/qiime/trunk/debian: . patches scripts scripts/shell
Andreas Tille
tille at moszumanska.debian.org
Wed Jul 29 12:28:45 UTC 2015
Author: tille
Date: 2015-07-29 12:28:44 +0000 (Wed, 29 Jul 2015)
New Revision: 19739
Added:
trunk/packages/qiime/trunk/debian/patches/allow_empty_default_taxonomy.patch
trunk/packages/qiime/trunk/debian/patches/call_renamed_seqprep_sortmerna.patch
Removed:
trunk/packages/qiime/trunk/debian/scripts/qiime_config
trunk/packages/qiime/trunk/debian/scripts/shell/qiime_help
trunk/packages/qiime/trunk/debian/scripts/usearch61
Modified:
trunk/packages/qiime/trunk/debian/control
trunk/packages/qiime/trunk/debian/get-orig-source
trunk/packages/qiime/trunk/debian/patches/check_config_file_in_new_location.patch
trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files.patch
trunk/packages/qiime/trunk/debian/patches/fix_script_usage_tests.patch
trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier.patch
trunk/packages/qiime/trunk/debian/patches/prevent_download_on_builds.patch
trunk/packages/qiime/trunk/debian/patches/prevent_google_addsense.patch
trunk/packages/qiime/trunk/debian/patches/relax_mothur_blast_raxml_versions.patch
trunk/packages/qiime/trunk/debian/patches/series
trunk/packages/qiime/trunk/debian/qiime-data.install
trunk/packages/qiime/trunk/debian/qiime.docs
trunk/packages/qiime/trunk/debian/qiime.install
trunk/packages/qiime/trunk/debian/rules
trunk/packages/qiime/trunk/debian/scripts/qiime
trunk/packages/qiime/trunk/debian/scripts/shell/.bashrc
trunk/packages/qiime/trunk/debian/scripts/shell/.zshrc
trunk/packages/qiime/trunk/debian/scripts/shell/qiime_environment
trunk/packages/qiime/trunk/debian/scripts/usearch
Log:
Commit all changes done by BioLinux in one rush
Modified: trunk/packages/qiime/trunk/debian/control
===================================================================
--- trunk/packages/qiime/trunk/debian/control 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/control 2015-07-29 12:28:44 UTC (rev 19739)
@@ -7,11 +7,14 @@
Priority: optional
Build-Depends: debhelper (>= 9),
python-all-dev (>= 2.7),
+ python-qcli,
python-cogent (>= 1.5.3),
python-numpy,
python-matplotlib,
+ python-setuptools,
ghc,
- python-sphinx
+ python-sphinx,
+ ruby-ronn
Standards-Version: 3.9.5
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/qiime/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/qiime/trunk/
@@ -24,33 +27,46 @@
${misc:Depends},
${python:Depends},
pynast (>= 1.2.2),
+ python-burrito (>= 0.9.0),
+ python-burrito-fillings (>= 0.1.0),
+ python-biom-format (>= 2.1),
python-cogent (>= 1.5.3),
- king,
- python-biom-format (>= 1.2.0),
+ python-matplotlib,
+ python-mpi4py,
+ python-numpy,
+ python-pandas (>= 0.13.1),
+ python-qcli,
+ qiime-data,
+ qiime-default-reference,
+ ampliconnoise,
+ blast2 | blast+-legacy,
+ bwa,
+ cd-hit,
+ chimeraslayer,
+ clearcut,
+ clustalw,
+ ea-utils,
+ emperor (>= 0.9.51),
fasttree,
- python-qcli,
+ infernal,
libjs-jquery,
- ea-utils,
- python-matplotlib,
- python-numpy
-Recommends: blast2 | blast+-legacy,
- cd-hit,
- chimeraslayer,
- muscle,
- infernal,
- ampliconnoise,
- parsinsert,
- clearcut,
- qiime-data,
- python-mpi4py,
- r-cran-optparse
+ mafft,
+ muscle,
+ parsinsert,
+ raxml,
+ r-cran-optparse,
+ rdp-classifier,
+ seqprep,
+ sortmerna,
+ sumatra,
+ swarm,
+ vsearch (>= 1.1.1)
+Recommends: mothur,
+ rtax
Suggests: t-coffee,
cytoscape,
- emperor,
- rdp-classifier,
torque-client
-Conflicts: denoiser,
- rdp-classifier ( >= 2.9 )
+Conflicts: denoiser
Provides: denoiser
Replaces: denoiser
Description: Quantitative Insights Into Microbial Ecology
@@ -61,9 +77,7 @@
* Sanger,
* Roche/454, and
* Illumina GAIIx.
- With all the underlying tools installed,
- of which not all are yet available in Debian (or any other Linux
- distribution), QIIME can perform
+ QIIME can perform:
* library de-multiplexing and quality filtering;
* denoising with PyroNoise;
* OTU and representative set picking with uclust, cdhit, mothur, BLAST,
@@ -100,11 +114,9 @@
have become standard in the field. A standard QIIME analysis begins with
sequence data from one or more sequencing platforms, including
* Sanger,
- * Roche/454, and
+ * Roche/454, and
* Illumina GAIIx.
- With all the underlying tools installed,
- of which not all are yet available in Debian (or any other Linux
- distribution), QIIME can perform
+ QIIME can perform:
* library de-multiplexing and quality filtering;
* denoising with PyroNoise;
* OTU and representative set picking with uclust, cdhit, mothur, BLAST,
Modified: trunk/packages/qiime/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/qiime/trunk/debian/get-orig-source 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/get-orig-source 2015-07-29 12:28:44 UTC (rev 19739)
@@ -1,5 +1,5 @@
#!/bin/sh
-# get source for king and strip binary JARs
+# strip binary JARs
COMPRESSION=xz
Added: trunk/packages/qiime/trunk/debian/patches/allow_empty_default_taxonomy.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/allow_empty_default_taxonomy.patch (rev 0)
+++ trunk/packages/qiime/trunk/debian/patches/allow_empty_default_taxonomy.patch 2015-07-29 12:28:44 UTC (rev 19739)
@@ -0,0 +1,22 @@
+The behaviour in qiime/assign_taxonomy.py is that if the taxonomy file path is
+not set then the RDP classifier will not be retrained.
+But the script bin/assign_taxonomy.py detects if the parameter is set to None
+and replaces it with the default value.
+So you always end up retraining the classifier, which is stupid.
+This is a nasty but effective workaround.
+--- a/scripts/assign_taxonomy.py
++++ b/scripts/assign_taxonomy.py
+@@ -106,6 +106,13 @@
+ default_reference_seqs_fp = qiime_config['assign_taxonomy_reference_seqs_fp']
+ default_id_to_taxonomy_fp = qiime_config['assign_taxonomy_id_to_taxonomy_fp']
+
++# Setting a path that begins with '#' disables the option
++if default_reference_seqs_fp.lstrip().startswith('#'):
++ default_reference_seqs_fp = None
++if default_id_to_taxonomy_fp.lstrip().startswith('#'):
++ default_id_to_taxonomy_fp = None
++
++
+ script_info['optional_options'] = [
+ make_option('-t', '--id_to_taxonomy_fp', type="existing_filepath",
+ help='Path to tab-delimited file mapping sequences to assigned '
Added: trunk/packages/qiime/trunk/debian/patches/call_renamed_seqprep_sortmerna.patch
===================================================================
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 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/patches/check_config_file_in_new_location.patch 2015-07-29 12:28:44 UTC (rev 19739)
@@ -3,13 +3,13 @@
--- a/scripts/print_qiime_config.py
+++ b/scripts/print_qiime_config.py
-@@ -210,8 +210,7 @@ class QIIMEConfig(TestCase):
- """local qiime_config has no extra params"""
-
+@@ -283,8 +283,7 @@
+ "config file as they will be ignored by QIIME.")
+
qiime_project_dir = get_qiime_project_dir()
- orig_config = parse_qiime_config_file(open(qiime_project_dir +
-- '/qiime/support_files/qiime_config'))
+- '/qiime/support_files/qiime_config'))
+ orig_config = parse_qiime_config_file(open('/etc/qiime/qiime_config'))
-
- #check the env qiime_config
+
+ # check the env qiime_config
qiime_config_env_filepath = getenv('QIIME_CONFIG_FP')
Modified: trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files.patch 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files.patch 2015-07-29 12:28:44 UTC (rev 19739)
@@ -6,15 +6,21 @@
--- a/qiime/util.py
+++ b/qiime/util.py
-@@ -302,8 +302,9 @@ def get_qiime_project_dir():
- # Get the directory containing util.py
- current_dir_path = dirname(current_file_path)
- # Return the directory containing the directory containing util.py
+@@ -268,14 +268,10 @@
+
+ def get_qiime_project_dir():
+ """ Returns the top-level QIIME directory
+- """
+- # Get the full path of util.py
+- current_file_path = abspath(__file__)
+- # Get the directory containing util.py
+- current_dir_path = dirname(current_file_path)
+- # Return the directory containing the directory containing util.py
- return dirname(current_dir_path)
--
-+ # In Debian what we actually want is /usr/lib/[qiime]
+
++ In Debian we know this is always /usr/lib/[qiime]
++ """
+ return "/usr/lib"
-+
+
def get_qiime_scripts_dir():
- """ Returns the QIIME scripts directory
-
+ """Return the directory containing QIIME scripts.
Modified: trunk/packages/qiime/trunk/debian/patches/fix_script_usage_tests.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_script_usage_tests.patch 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/patches/fix_script_usage_tests.patch 2015-07-29 12:28:44 UTC (rev 19739)
@@ -4,35 +4,35 @@
--- a/qiime/test.py
+++ b/qiime/test.py
-@@ -14,7 +14,7 @@ from os.path import isdir, split, join,
+@@ -15,7 +15,7 @@
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 @@ def run_script_usage_tests(test_data_dir
- 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 = []
+ from traceback import format_exc
+ from skbio.util import remove_files
+@@ -806,7 +806,9 @@
+ self._log('Scripts to test:\n %s' % ' '.join(scripts))
+ self._log('')
+
+- 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
+
+ for script_name in scripts:
+ self.total_scripts += 1
--- a/tests/all_tests.py
+++ b/tests/all_tests.py
-@@ -94,6 +94,9 @@ def main():
+@@ -96,6 +96,9 @@
bad_tests.append(unittest_name)
- qiime_test_data_dir = join(get_qiime_project_dir(),'qiime_test_data')
+ 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:
+ if opts.script_usage_tests is not None:
Modified: trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier.patch 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier.patch 2015-07-29 12:28:44 UTC (rev 19739)
@@ -7,16 +7,16 @@
--- a/qiime/assign_taxonomy.py
+++ b/qiime/assign_taxonomy.py
-@@ -65,14 +65,20 @@ def validate_rdp_version(rdp_jarpath=Non
+@@ -54,14 +54,19 @@
"http://qiime.org/install/install.html#rdp-install"
- )
+ )
- rdp_jarname = os.path.basename(rdp_jarpath)
- version_match = re.search("\d\.\d", rdp_jarname)
- if version_match is None:
- raise RuntimeError(
- "Unable to detect RDP Classifier version in file %s" % rdp_jarname
-- )
+- )
+ #Patch for Bio-Linux/Debian. Allow us to reassure QIIME about the version
+ #of RDP Classifier using an environment variable.
+ if os.getenv('RDP_JAR_VERSION_OK') is not None :
@@ -28,8 +28,7 @@
+ raise RuntimeError(
+ "Unable to detect RDP Classifier version in file %s" % rdp_jarname
+ )
-+
-+ version = float(version_match.group())
++ version = float(version_match.group())
- version = float(version_match.group())
if version < 2.1:
@@ -37,8 +36,8 @@
"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():
- params['training_data_properties_fp'] = opts.training_data_properties_fp
+@@ -366,6 +366,11 @@
+ 'training_data_properties_fp'] = opts.training_data_properties_fp
params['max_memory'] = "%sM" % opts.rdp_max_memory
+ #Record actual RDP version. This shouldn't fail as it was called once
@@ -47,5 +46,5 @@
+
+
elif assignment_method == 'rtax':
- params['id_to_taxonomy_fp'] = opts.id_to_taxonomy_fp
- params['reference_sequences_fp'] = opts.reference_seqs_fp
+ params['id_to_taxonomy_fp'] = opts.id_to_taxonomy_fp
+ params['reference_sequences_fp'] = opts.reference_seqs_fp
Modified: trunk/packages/qiime/trunk/debian/patches/prevent_download_on_builds.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/prevent_download_on_builds.patch 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/patches/prevent_download_on_builds.patch 2015-07-29 12:28:44 UTC (rev 19739)
@@ -4,27 +4,15 @@
--- a/setup.py
+++ b/setup.py
-@@ -132,6 +132,9 @@ def build_FastTree():
- def download_UCLUST():
- """Download the UCLUST executable and set it to the scripts directory"""
+@@ -358,9 +358,8 @@
+ chdir(cwd)
-+ print "It is not possible to download anything at package install time."
-+ return '/usr/lib/qiime/bin/uclust' # path to installed helper script
-+ # The following lines will be ignored
- if platform == 'darwin':
- URL = 'http://www.drive5.com/uclust/uclustq1.2.22_i86darwin64'
- elif platform == 'linux2':
-@@ -175,13 +178,6 @@ if build_stack:
- 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 = """
+-# don't build any of the non-Python dependencies if the following modes are
+-# invoked
+-if all([e not in sys.argv for e in 'egg_info', 'sdist', 'register']):
++# don't build any of the non-Python dependencies - let DPKG handle it
++if False:
+ catch_install_errors(build_denoiser, 'denoiser')
+ catch_install_errors(download_UCLUST, 'UCLUST')
+ catch_install_errors(build_FastTree, 'FastTree')
Modified: trunk/packages/qiime/trunk/debian/patches/prevent_google_addsense.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/prevent_google_addsense.patch 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/patches/prevent_google_addsense.patch 2015-07-29 12:28:44 UTC (rev 19739)
@@ -8,14 +8,14 @@
+++ b/doc/_templates/layout.html
@@ -2,8 +2,6 @@
- {% block extrahead %}
+ {% block extrahead %}
<meta http-equiv="Content-Style-Type" content="text/css" />
-<script type="text/javascript" src="http://www.google.com/jsapi?key=ABQIAAAAbW_pA971hrPgosv-Msv7hRRE2viNBUPuU405tK6p2cguOFmlFBQSwZMG6_q_v6Z42nkdo9ejT1aHmA"></script>
-<script type="text/javascript" src="{{ pathto("_static/google_feed.js",1)}}"></script>
{% endblock %}
{% block relbar1 %}
-@@ -43,12 +41,8 @@ pathto("_static/PoweredByPycogent.jpg",
+@@ -47,10 +45,6 @@
<br /></div>
{{ super() }}
<script type="text/javascript">
@@ -26,7 +26,3 @@
try {
var pageTracker = _gat._getTracker("UA-6636235-4");
pageTracker._trackPageview();
- } catch(err) {}</script>
--{% endblock %}
-\ No newline at end of file
-+{% endblock %}
Modified: trunk/packages/qiime/trunk/debian/patches/relax_mothur_blast_raxml_versions.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/relax_mothur_blast_raxml_versions.patch 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/patches/relax_mothur_blast_raxml_versions.patch 2015-07-29 12:28:44 UTC (rev 19739)
@@ -4,30 +4,57 @@
--- a/scripts/print_qiime_config.py
+++ b/scripts/print_qiime_config.py
-@@ -467,7 +467,7 @@ class QIIMEDependencyFull(QIIMEDependenc
+@@ -326,7 +326,7 @@
+ version_string = stdout.strip().split('v')[-1].strip('q')
+ 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
+@@ -360,7 +360,7 @@
+
+ try:
+ version = tuple(map(int, version_str.split('.')))
+- pass_test = version == acceptable_version
++ pass_test = version >= acceptable_version
+ except ValueError:
+ pass_test = False
+
+@@ -460,7 +460,7 @@
version_string = stdout.strip().split(' ')[1].strip()
try:
- version = tuple(map(int,version_string.split('.')))
+ 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 @@ class QIIMEDependencyFull(QIIMEDependenc
+@@ -481,7 +481,7 @@
+ version_string = stdout.strip().split(' ')[2].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
+@@ -548,7 +548,7 @@
version_string = stdout.strip().split(' ')[1].strip('v.')
try:
- version = tuple(map(int,version_string.split('.')))
+ 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 @@ class QIIMEDependencyFull(QIIMEDependenc
+@@ -573,7 +573,7 @@
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.")
+- acceptable_version = [(7, 3, 0), (7, 3, 0)]
++ acceptable_version = [(7, 3, 0), (7, 3, 5)]
+ self.assertTrue(which('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 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/patches/series 2015-07-29 12:28:44 UTC (rev 19739)
@@ -1,10 +1,9 @@
+allow_empty_default_taxonomy.patch
check_config_file_in_new_location.patch
-fix_binary_helper_location.patch
make_qiime_accept_new_rdp_classifier.patch
fix_path_for_support_files.patch
-detect_matplotlib_version.patch
relax_mothur_blast_raxml_versions.patch
prevent_google_addsense.patch
fix_script_usage_tests.patch
prevent_download_on_builds.patch
-exclude_tests_that_need_to_fail.patch
+#exclude_tests_that_need_to_fail.patch
Modified: trunk/packages/qiime/trunk/debian/qiime-data.install
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime-data.install 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/qiime-data.install 2015-07-29 12:28:44 UTC (rev 19739)
@@ -1,2 +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
+#qiime_test_data/filter_alignment/lanemask_in_1s_and_0s /usr/share/qiime/data
Modified: trunk/packages/qiime/trunk/debian/qiime.docs
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.docs 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/qiime.docs 2015-07-29 12:28:44 UTC (rev 19739)
@@ -1 +1 @@
-README
+README.md
Modified: trunk/packages/qiime/trunk/debian/qiime.install
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.install 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/qiime.install 2015-07-29 12:28:44 UTC (rev 19739)
@@ -1,9 +1,10 @@
+debian/qiime_config etc/qiime
debian/scripts/qiime usr/bin
debian/scripts/shell/* usr/lib/qiime/shell
debian/scripts/shell/.[bz]* usr/lib/qiime/shell
-debian/scripts/qiime_config etc/qiime
debian/scripts/uclust usr/lib/qiime/bin
debian/scripts/usearch* usr/lib/qiime/bin
+debian/scripts/print* 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
Modified: trunk/packages/qiime/trunk/debian/rules
===================================================================
--- trunk/packages/qiime/trunk/debian/rules 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/rules 2015-07-29 12:28:44 UTC (rev 19739)
@@ -9,11 +9,8 @@
pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
-#Allowing this to be overridden by environemnt helps with backports
-DEB_PYTHON_SUPPORT?=python2
-
%:
- dh $@ --with $(DEB_PYTHON_SUPPORT)
+ dh $@ --with python2
override_dh_compress:
dh_compress \
@@ -23,14 +20,21 @@
--exclude=.fna \
--exclude=.fna.txt
+override_dh_auto_build:
+ cd qiime/support_files/denoiser/FlowgramAlignment && make
+ cd doc && make html
+ ronn -r --manual=QIIME --organization='Bio-Linux' debian/qiime.1.ronn
+ dh_auto_build
+
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
- rm -f $(pkg)/support_files/denoiser/bin/*
+ rm -f debian/*.1
+ ( cd qiime/support_files/denoiser/FlowgramAlignment && make clean ) || true
+ rm -f qiime/support_files/denoiser/bin/*
#In case the tarball was not re-packed, remove any .jars
find -name '*.jar' -delete
#And in case any Python script was run, remove the .pyc
@@ -38,6 +42,7 @@
# Remove remainings from running the test suite
rm -f BLAST_temp_db*
rm -rf jobs tests/jobs
+ rm -rf qiime.egg-info
export ROOTDIR=debian/$(pkg)
Modified: trunk/packages/qiime/trunk/debian/scripts/qiime
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/qiime 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/scripts/qiime 2015-07-29 12:28:44 UTC (rev 19739)
@@ -35,19 +35,26 @@
Setting up $QSNAME environment to run QIIME commands.
You have QIIME version $QIIME_VERSION.
-Type 'help' for more info, 'exit' to return to regular shell.
+Note that this will not produce identical results to the official QIIME release
+as it uses updated versions of several tools.
+
+Type 'help' for help, 'print_qiime_config_all' to see the current QIIME
+settings, or 'exit' to return to regular shell.
"""
eval exec $QIIMESHELL
+elif [ "$1" = help ] ; then
+ echo "Type 'man qiime' for help."
else
#Just run the command
-
- # Set environment
+
+ # Set environment
. /usr/lib/qiime/shell/qiime_environment
- cmd=`basename "$1" .py`.py
+ cmd=/usr/lib/qiime/bin/`basename "$1" .py`
shift
- exec "/usr/lib/qiime/bin/$cmd" "$@"
-fi
+ [ -e "$cmd" ] || cmd="${cmd}.py"
+ exec "$cmd" "$@"
+fi
Deleted: trunk/packages/qiime/trunk/debian/scripts/qiime_config
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/qiime_config 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/scripts/qiime_config 2015-07-29 12:28:44 UTC (rev 19739)
@@ -1,20 +0,0 @@
-# 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 $QIIME_CONFIG_FP and edit that copy of the file.
-
-# This file refers to default GreenGenes data files installed by the qiime-data
-# package.
-
-cluster_jobs_fp
-python_exe_fp python
-working_dir .
-blastmat_dir /usr/share/ncbi/data
-blastall_fp blastall
-pynast_template_alignment_fp /usr/share/qiime/data/core_set_aligned.fasta.imputed
-template_alignment_lanemask_fp /usr/share/qiime/data/lanemask_in_1s_and_0s
-pynast_template_alignment_blastdb
-jobs_to_start 1
-seconds_to_sleep 60
-qiime_scripts_dir /usr/lib/qiime/bin/
-temp_dir /tmp
Modified: trunk/packages/qiime/trunk/debian/scripts/shell/.bashrc
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/shell/.bashrc 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/scripts/shell/.bashrc 2015-07-29 12:28:44 UTC (rev 19739)
@@ -3,10 +3,7 @@
test -e "/etc/bash.bashrc" && source "/etc/bash.bashrc"
test -e "~/.bashrc" && source "~/.bashrc"
-help()
-{
- cat "$QIIME_HELP_TEXT"
-}
+alias help='man qiime'
source /usr/lib/qiime/shell/qiime_environment
PS1="$PS1 qiime > "
Modified: trunk/packages/qiime/trunk/debian/scripts/shell/.zshrc
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/shell/.zshrc 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/scripts/shell/.zshrc 2015-07-29 12:28:44 UTC (rev 19739)
@@ -6,9 +6,6 @@
source /usr/lib/qiime/shell/qiime_environment
-help()
-{
- cat "$QIIME_HELP_TEXT"
-}
+alias help='man qiime'
PROMPT="$PROMPT qiime > "
Modified: trunk/packages/qiime/trunk/debian/scripts/shell/qiime_environment
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/shell/qiime_environment 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/scripts/shell/qiime_environment 2015-07-29 12:28:44 UTC (rev 19739)
@@ -6,7 +6,8 @@
# This file needs to be readable by /bin/sh and zsh so no bash-isms allowed.
export PYTHONPATH=$PYTHONPATH/:/usr/share/pyshared/qiime
-export PATH="$PATH:/usr/lib/qiime/bin:/usr/share/ampliconnoise/Scripts:/usr/lib/ChimeraSlayer"
+export PATH="$PATH:/usr/lib/qiime/bin:/usr/lib/qiime/support_files/denoiser/bin/FlowgramAli_4frame"
+export PATH="$PATH:/usr/share/ampliconnoise/Scripts:/usr/lib/ChimeraSlayer"
export QIIME_HELP_TEXT=/usr/lib/qiime/shell/qiime_help
export QIIME_CONFIG_FP=${QIIME_CONFIG_FP:-/etc/qiime/qiime_config}
export BLASTMAT=${BLASTMAT:-/usr/share/ncbi/data}
Deleted: trunk/packages/qiime/trunk/debian/scripts/shell/qiime_help
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/shell/qiime_help 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/scripts/shell/qiime_help 2015-07-29 12:28:44 UTC (rev 19739)
@@ -1,50 +0,0 @@
-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 any QIIME command such as validate_mapping_file.py:
-
- $ qiime validate_mapping_file [...]
-
- or just type 'qiime' to get a 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.
-
-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.
-
-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.
-
-UCLUST and USEARCH:
-
- 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:
-
- http://qiime.org
Modified: trunk/packages/qiime/trunk/debian/scripts/usearch
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/usearch 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/scripts/usearch 2015-07-29 12:28:44 UTC (rev 19739)
@@ -2,7 +2,7 @@
#
# Added by Tim Booth <tbooth at ceh.ac.uk>
# QIIME wants very much to use the USEARCH binary, but this is not free software.
-# However, it is available right now free-of-charge if you only want the
+# However, it is available right now free-of-charge if you only want the
# 32-bit version.
# Redistribution requires a licence, which I could apply for, but then nobody
# but me can redistribute BL, which is no good!
@@ -14,8 +14,9 @@
echo """\r\
USEARCH is not freely redistributable and is thus not included in the
-default QIIME package.
-You may obtain a personal copy of the 32-bit program at no charge.
+default QIIME package. The free VSEARCH will be used in place of USEARCH
+where possible, but this does not produce identical results.
+You may obtain a personal copy of the 32-bit USEARCH at no charge.
To use this feature, please go to:
http://www.drive5.com/usearch/download.html
Deleted: trunk/packages/qiime/trunk/debian/scripts/usearch61
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/usearch61 2015-07-29 10:22:50 UTC (rev 19738)
+++ trunk/packages/qiime/trunk/debian/scripts/usearch61 2015-07-29 12:28:44 UTC (rev 19739)
@@ -1,29 +0,0 @@
-#!/bin/sh
-#
-# Added by Tim Booth <tbooth at ceh.ac.uk>
-# QIIME wants very much to use the USEARCH binary, but this is not free software.
-# However, it is available right now free-of-charge if you only want the
-# 32-bit version.
-# Redistribution requires a licence, which I could apply for, but then nobody
-# but me can redistribute BL, which is no good!
-
-# See if usearch.real is available anywhere
-if which usearch61.real >/dev/null ; then
- exec usearch61.real "$@"
-fi
-
-echo """\r\
-USEARCH 6 is not freely redistributable and is thus not included in the
-default QIIME package.
-You may obtain a personal copy of the 32-bit program at no charge.
-
-To use this feature, please go to:
- http://www.drive5.com/usearch/download.html
-
-Download USEARCH v6.1, then:
- sudo mv usearch* /usr/local/bin/usearch61
- sudo chmod a+x /usr/local/bin/usearch61
-
-You probably also want to install USEARCH 5 as /usr/local/bin/usearch
-"""
-exit 1
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