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OPTIONS
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The configuration file consists of a single [global] section, a single
[dependencies] section, and any number of data sections or applications
sections. All application and data sections must have unique names. All data
sections must begin with data-
Configuration file options:
[global]
final-deploy-directory [REQUIRED]
Supported values: the full path to the deploy directory
Description: The base directory that all applications will be deployed
into. Applications will be in directories with the name:
applicationname-version-release (or repository) depending
on the install type.
log-level
Supported values: DEBUG, INFO
Default value: INFO
Description: DEBUG provides more verbose output then INFO.
max-deploy-threads
Supported values: positive integer (e.g. 1, 2, 3, 4)
Default value: 2
Description: Number of deploy threads (does not include the main
thread)
python-exe
Supported values: full path to a python executable
Description: This python executable will be used for any
python-distutils applications to build. If none is
specified qiime-deploy will default to bin/python of a
[python] application section or simply attempt to use
'python' found in the user's PATH.
r-exe
Supported values: full path to an R executable
Description: This R executable will be used for any
r-package applications to build via install.packages(). If
none is specified qiime-deploy will default to bin/R of an
[r] application section or simply attempt to use 'R' found
in the user's PATH.
append-environment-to-bashrc:
Supported values: yes, no
Default value: no
Description: If yes, the line sourcing activate.sh will be appended to
the end of ~/.bashrc so the environment will be activated
for interactive non-login shells.
append-environment-to-bashprofile:
Supported values: yes, no
Default value: no
Description: If yes, the line sourcing activate.sh will be appended to
the end of ~/.bash_profile so the environment will be activated
for login shells.
tmp-directory
Supported values: the full path to the base temp directory to be used
Description: The base directory that all applications will be
downloaded and compiled in.
[dependencies]
commands
Supported values: command names, separated by commas
Description: qiime-deploy will check all of the specified command names
to ensure that they are avaialble in the PATH
extra-bash-test
Supported values: a valid bash command to execute
Description: qiime-deploy will execute this bash command and deem it
successful if it returns 0. If it returns something
besides 0, the test will fail.
[data-*]
local-file [REQUIRED]
Description: This is the name of the local file. It will be placed in
final-deploy-directory.
remote-file [REQUIRED]
Description: The URL of the file to download.
data-file-environment-var-name
Description: The name of the environment variable to set with the full
path to the downloaded file, e.g.
/final-deploy-directory/local-file
[applications]
version [REQUIRED]
Description: The version of the application being deployed.
build-type [REQUIRED]
Supported values: autoconf, python-distutils, make, make-install,
c-file, cpp-file, ant, r-package, copy, custom
Description: The build type for the application.
autoconf: This is the standard GNU autoconf process (./configure;
make; make install). Contains the additional options
autoconf-configure-options and autoconf-make-options.
python-distutils: This is the standard python distutils process
(python setup.py build; python setup.py install).
Contains the additional options:
python-build-options. If the global option
deploy-in-python-site-packages is no then the
package will be deployed in its own directory and
PYTHONPATH will be modified. If the value is set
to yes, then the user executing qiime-deploy must
have the appropriate permissions to write to the
python's site-packages directory. The package
will be deployed using whichever python
qiime-deploy defaults to (e.g. either via the
python-exe setting, deploying a [python]
application as part of the qiime-deploy process,
or as a last case the 'python' in the user's
PATH).
make: This simply runs 'make' for the application. Contains the
additonal options: make-options. Because this operation
does not cause any installation of the appliation, the source
tree is simply copied to the final deploy directory.
make-install: This simply runs 'make' and then 'make install' for
the application. Contains the additonal options:
make-install-options for the make process. This does
not currently specify a prefix so the user must have
the appropriate permissions to deploy the application
in whatever location 'make install' defaults to.
c-file: Compile a single c file with gcc. Additional options:
c-file-compile-options, exe-name. Because this operation
does not cause any installation of the application, the
source tree is simply copied to the final deploy directory.
cpp-file: Compile a single C++ file using g++. Additional
options: cpp-file-compile-options, exe-name. Because
this operation does not cause any installation of the
application, the source tree is simply copied to the
final deploy directory.
ant: This simply runs 'ant' in the applications base directory.
r-package: This runs R's install.packages() function to obtain the
latest version of the package. The package will be
deployed using whichever R qiime-deploy defaults to
(e.g. either via the r-exe setting, deploying an [r]
application as part of the qiime-deploy process,
or as a last case the 'R' in the user's PATH). Requires
that r-package-name and r-package-repo are provided.
Will ignore the following options: release-file-name,
release-location, repository-type, repository-location,
repository-local-name, repository-options,
local-repository, unzipped-name, skip-unzipped-name, and
copy-source-to-final-deploy (in addition to other build-
type-specific options).
copy: This simply unzips (if needed) and copies the downloaed
application to the final deploy directory.
custom: This option performs a custom install. lib/custom.py must
be modified to support additional applications. Currently
supported applications: denoiser, uclust, r, pyronoise,
ampliconnoise, and dotur.
release-file-name [REQUIRED unless repository-* is specified or r-package build-type]
Description: This is the name of the file that will be downloaded from
release-location. Note: it will NOT be renamed to this.
release-file-name must match the name from
release-location.
release-location [REQUIRED unless repository-* is specified or r-package build-type]
Description: This is the location of the file to be downloaded. It must
be a single download location.
repository-type [REQUIRED unless release-* is specified or r-package build-type]
Description: The type of repository to checkout from. Currently
subversion (svn co) and git (git clone) are supported.
repository-location [REQUIRED unless release-* is specified or r-package build-type]
Description: Location of the repository to checkout the application.
See local-repository for more details.
repository-local-name [REQUIRED unless release-* is specified or r-package build-type]
Description: The name of the local directory that the repository should
be placed in. Ignored if local-repository is yes.
make-folderpath-relative-to-local
Description: The path starting from repository-local-name or release-file-name
to the subdirectory containing the Makefile. For example, if
repository-local-name is "dir", but the Makefile is located in
"dir/subdir1" then make-folderpath-relative-to-local would be
"subdir1".
repository-options
Description: These are passed to "svn co" for subversion and "git
clone" for git. Ignored if local-repository is yes.
local-repository
Supported values: yes, no
Default value: no
Description: If yes, repository-location is assumed to be an absolute
path on the local machine that points to a repository that
was previously cloned (if repository-type is git) or
checked out (if repository-type is svn). This absolute
path should be a directory. This directory will *never* be
removed or modified (a temporary copy will be made and the
build will happen there). repository-local-name and
repository-options will be ignored.
If no, repository-location is assumed to be a location
from which a local clone/checkout must first be made.
deploy-in-python-site-packages
Supported values: yes, no
Default value: no
Description: If yes, this will attempt to deploy any python-distutils
applications into the specifieds python's site-packages
directory instead of deploying into a directory in
final-deploy-directory and modifying PYTHONPATH.
Notes: The user account executing qiime-deploy must have the
appropriate priviledges to perform this operation.
unzipped-name
Description: The unzipped name of the release-file-name after unzipping
is performed. This defaults to the name of
release-file-name without the zip extension (e.g. .tar.gz,
.tgz, or .zip). However, if that is not the case then this
parameter must be set.
skip-unzipped-name
Supported values: yes or no
Default: no
Description: If the file specified by release-file-name does not unzip
to a separate directory then skip-unzipped-name must be
set. For example, if the file unzips to the current
directory, then this should be set to yes.
autoconf-configure-options
Description: Any additional flags that should be passed to the autoconf
configure command. --prefix is automatically generated and
set.
autoconf-make-options
Description: Any additional flags that should be passed to the autoconf
make command.
python-build-options
Description: Any additional flags that should be passed to the python
distutils build process. --prefix is automatically
generated and set.
python-install-options
Description: Any additional flags that should be passed to the python
distutils install process. --prefix is automatically
generated and set.
make-options
Description: Any additional flags that should be passed to the 'make'
for the make build-type.
make-install-options
Description: Any additional flags that should be passed to the 'make'
command for the make-install build-type.
c-file-compile-options
Description: Any additional flags that should be passed to the compile
command for the c-file build-type.
cpp-file-compile-options
Description: Any additional flags that should be passed to the compile
command for the cpp-file build-type.
exe-name
Description: The name of the exe to be generated by either the c-file
or cpp-file build-types.
r-package-name
Description: The name of the R package to be installed. REQUIRED if
build-type is r-package.
r-package-repo
Description: URL of the R package repository to download the
r-package-name package from. REQUIRED if build-type is
r-package.
post-bash-commands
Description: Any additional bash commands to execute after the entire
build process is complete and successful.
relative-directory-add-to-path
Description: Any directories for the application that should be added
to the user's PATH environment variable (e.g. bin/ or .).
This may be a comma separated list.
set-environment-variables-deploypath
Description: Set additional environment variables (PATH should be set
with relative-directory-add-to-path) using the format
ENV_NAME=ENV_VALUE, separated by commas. Relative paths,
from the base deploy directory for the application, should
be used for ENV_VALUE since the full path will be
determined automatically.
set-environment-variables-value
Description: Set additional environment variables to a specific value,
i.e. not a relative path, in the format:
ENV_NAME=ENV_VALUE, with multiple items separated by
commas.
copy-source-to-final-deploy
Supported values: yes or no
Default: no
Description: If after the build process the source directory should be
copied to the final deploy directory for the particular
application, this may be set to yes.
deps
Description: Dependencies required by the application. This can be a
comma separated list. It must be application names
specified in this file. data-* sections cannot currently
be used as dependencies.
An example: deploying [matplotlib] may require a custom
[python] and [numpy] to be deployed first, in that
case matplotlib would list the dependencies as following:
deps: python, numpy