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Added conf files for the development versions of biom-format, PrimerP…

…rospector, PyNAST, and PyCogent.
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1 parent d3926b9 commit e6de5ad8691d0116398f2fd218648dd3a6ea6cb5 @jairideout jairideout committed Nov 13, 2012
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-qiime-deploy-conf
-=================
+# qiime-deploy-conf
-Configuration files to be used with the qiime-deploy packages.
+Configuration files to be used with the
+[qiime-deploy](https://github.com/qiime/qiime-deploy) tool. For more details on
+how to use these configuration files with _qiime-deploy_, please refer to the
+README on the _qiime-deploy_ project page.
-Options
--------
+## Options
For a complete description of all options and file layout, please see the
OPTIONS file.
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+qiime-deploy-conf
+=================
+
+configuration files to be used for biom-format 1.0.0-dev.
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+##############################################################################
+#
+# biom-format.conf
+#
+# qiime-deploy configuration file
+# This file specifies the applications to download and deploy.
+#
+# This file contains a single [global] section and a single [dependencies]
+# section as well as any number of data or application sections. Each section
+# must have a unique name. Data sections must begin with data-
+#
+# See the OPTIONS file for a description of each option.
+#
+##############################################################################
+
+[dependencies]
+commands: gcc, g++, java, javac, ant
+
+[global]
+log-level: INFO
+max-deploy-threads: 6
+append-environment-to-bashrc: yes
+append-environment-to-bashprofile: no
+
+[python]
+version: 2.7.1
+build-type: autoconf
+release-file-name: Python-2.7.1.tgz
+release-location: ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7.1.tgz
+relative-directory-add-to-path: bin
+#autoconf-make-options: -j4
+autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 --enable-unicode=ucs4
+
+[numpy]
+version: 1.5.1
+build-type: python-distutils
+release-file-name: numpy-1.5.1.tar.gz
+release-location: http://sourceforge.net/projects/numpy/files/NumPy/1.5.1/numpy-1.5.1.tar.gz
+deps: python
+
+[biom-format]
+version: 1.0.0
+build-type: copy
+repository-local-name: biom-format
+repository-location: git://github.com/biom-format/biom-format.git
+repository-type: git
+deps: python, numpy
+set-environment-variables-deploypath: PYTHONPATH=python-code/
+relative-directory-add-to-path: scripts/
+
+[setuptools]
+version: 0.6c11
+build-type: python-distutils
+release-file-name: setuptools-0.6c11.tar.gz
+release-location: http://pypi.python.org/packages/source/s/setuptools/setuptools-0.6c11.tar.gz
+deps: python
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+qiime-deploy-conf
+=================
+
+configuration files to be used for PrimerProspector 1.0.1-dev.
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+##############################################################################
+#
+# primer-prospector.conf
+#
+# qiime-deploy configuration file
+# This file specifies the applications to download and deploy.
+#
+# This file contains a single [global] section and a single [dependencies]
+# section as well as any number of data or application sections. Each section
+# must have a unique name. Data sections must begin with data-
+#
+# See the OPTIONS file for a description of each option.
+#
+##############################################################################
+
+[dependencies]
+commands: gcc, g++, java, javac, ant
+
+[global]
+log-level: INFO
+max-deploy-threads: 6
+append-environment-to-bashrc: yes
+append-environment-to-bashprofile: no
+
+[python]
+version: 2.7.1
+build-type: autoconf
+release-file-name: Python-2.7.1.tgz
+release-location: ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7.1.tgz
+relative-directory-add-to-path: bin
+#autoconf-make-options: -j4
+autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 --enable-unicode=ucs4
+
+[pycogent]
+version: 1.5.3
+build-type: python-distutils
+release-file-name: PyCogent-1.5.3.tgz
+set-environment-variables-value: TEST_DB=1
+copy-source-to-final-deploy: yes
+release-location: http://downloads.sourceforge.net/project/pycogent/PyCogent/1.5.3/PyCogent-1.5.3.tgz
+deps: numpy
+set-environment-variables-deploypath: PYCOGENT=./
+
+[numpy]
+version: 1.5.1
+build-type: python-distutils
+release-file-name: numpy-1.5.1.tar.gz
+release-location: http://sourceforge.net/projects/numpy/files/NumPy/1.5.1/numpy-1.5.1.tar.gz
+deps: python
+
+[matplotlib]
+version: 1.1.0
+build-type: python-distutils
+release-file-name: matplotlib-1.1.0.tar.gz
+release-location: http://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.1.0/matplotlib-1.1.0.tar.gz
+deps: numpy
+
+[rdpclassifier]
+version: 2.2
+build-type: copy
+release-file-name: rdp_classifier_2.2.zip
+unzipped-name: rdp_classifier_2.2
+release-location: http://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.2.zip
+relative-directory-add-to-path: .
+set-environment-variables-deploypath: RDP_JAR_PATH=rdp_classifier-2.2.jar
+
+[vienna]
+version: 1.8.4
+build-type: custom
+release-file-name: ViennaRNA-1.8.4.tar.gz
+unzipped-name: ViennaRNA-1.8.4
+release-location: http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.8.4.tar.gz
+autoconf-configure-options: --without-perl
+relative-directory-add-to-path: bin
+
+[pprospector]
+version: 1.0.1
+build-type: python-distutils
+repository-local-name: pprospector
+repository-location: https://pprospector.svn.sourceforge.net/svnroot/pprospector/trunk
+repository-type: svn
+repository-options: --trust-server-cert --non-interactive
+copy-source-to-final-deploy: yes
+relative-directory-add-to-path: bin
+deps: pycogent
+
+[setuptools]
+version: 0.6c11
+build-type: python-distutils
+release-file-name: setuptools-0.6c11.tar.gz
+release-location: http://pypi.python.org/packages/source/s/setuptools/setuptools-0.6c11.tar.gz
+deps: python
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+qiime-deploy-conf
+=================
+
+configuration files to be used for PyCogent 1.5.3-dev.
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