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---
#
# THIS FILE IS DEPRECATED
#
# See https://github.com/galaxyproject/starforge-recipes
#
packages:
biopython:
version: 1.66
prebuild:
wheel: "for py in /python/cp*-`uname -m`; do ${py}/bin/easy_install pip; ${py}/bin/pip install --upgrade pip ; ${py}/bin/pip install --index-url https://wheels.galaxyproject.org/simple/ numpy || exit 1; done"
insert_setuptools: true
bx-python:
version: 0.8.1
prebuild:
wheel: "for py in /python/cp*-`uname -m`; do ${py}/bin/pip install --index-url https://wheels.galaxyproject.org/simple/ numpy python-lzo || exit 1; done"
apt:
- git
yum:
# manylinux1 images don't preinstall these, which is probably the
# way they should all work
- zlib-devel
Cheetah3:
version: 3.1.0
MarkupSafe:
version: 1.0
mercurial:
version: 3.7.3
insert_setuptools: true
netifaces:
version: 0.10.6
numpy:
version: 1.9.2
yum:
- atlas-devel
psutil:
version: 5.4.3
psycopg2:
version: 2.6.1
src:
- http://initd.org/psycopg/tarballs/PSYCOPG-2-6/psycopg2-2.6.1.tar.gz
insert_setuptools: true
prebuild: curl -LO http://yum.postgresql.org/9.5/redhat/rhel-5-x86_64/pgdg-centos95-9.5-2.noarch.rpm && rpm -i pgdg-centos95-9.5-2.noarch.rpm && yum install -y postgresql95-devel && sed -i -e 's%^#pg_config=.*%pg_config=/usr/pgsql-9.5/bin/pg_config%' ${SRC_ROOT}/setup.cfg
#apt:
# - libpq-dev
#yum:
# - postgresql-devel
#zypper:
# - postgresql-devel
#brew:
# - postgresql
pycrypto:
version: 2.6.1
insert_setuptools: true
pysam:
version: 0.14.1
prebuild:
wheel: >
sed -i'' -e 's/^HTSLIB_CONFIGURE_OPTIONS = .*/HTSLIB_CONFIGURE_OPTIONS = "--disable-libcurl"/' ${SRC_ROOT}/setup.py;
for py in /python/cp*-`uname -m`; do
${py}/bin/pip install 'cython' || exit 1;
done
auditwheel_args: 'repair -w dist -L .'
# manylinux1 x86_64 wheels are in PyPI
imageset: linux32-macos-wheel
brew:
- xz
yum:
- bzip2-devel
- xz-devel
- zlib-devel
pysqlite:
# pysqlite is dropped because SQLAlchemy will just use sqlite3 from
# Python's stdlib, but keeping the rule here in case we have to add it
# back (people with non-standard Pythons may be missing sqlite3 if the
# sqlite3 headers were not available at Python compile-time).
version: 2.7.0
src:
- https://sqlite.org/2015/sqlite-autoconf-3081002.tar.gz
prebuild:
wheel: for f in sqlite3.h sqlite3.c sqlite3ext.h; do cp ${SRC_ROOT_1}/$f $f || return 1; done && echo 'include_dirs=.' >>${SRC_ROOT_0}/setup.cfg
build_args: build_static bdist_wheel
python-ldap:
version: 2.4.44
src:
- https://gmplib.org/download/gmp/gmp-6.1.2.tar.bz2
- https://ftp.gnu.org/gnu/nettle/nettle-3.3.tar.gz
- https://www.gnupg.org/ftp/gcrypt/gnutls/v3.5/gnutls-3.5.15.tar.xz
- http://www.openssl.org/source/openssl-1.0.2l.tar.gz
- http://www.openldap.org/software/download/OpenLDAP/openldap-release/openldap-2.4.45.tgz
prebuild:
wheel: >
if [ `uname -s` == 'Darwin' ] ; then
sed -e 's/^library_dirs.*//' -e 's#^include_dirs.*#include_dirs = /Developer/SDKs/MacOSX10.6.sdk/usr/include /Developer/SDKs/MacOSX10.6.sdk/usr/include/sasl#' -i .orig ${SRC_ROOT_0}/setup.cfg ;
sed -e $'$i\\\n#define LDAP_VLV_ERROR 0x4C\n' -i .orig ${SRC_ROOT_0}/Modules/errors.h ;
else
cd $SRC_ROOT_1 ;
./configure ;
make ;
make install ;
cd $SRC_ROOT_2 ;
./configure ;
make ;
make install ;
export PKG_CONFIG_PATH=/usr/local/lib64/pkgconfig/:$PKG_CONFIG_PATH ;
cd $SRC_ROOT_3 ;
./configure --with-included-libtasn1 --with-included-unistring --without-p11-ki ;
make ;
make install ;
cd $SRC_ROOT_4 ;
./config shared enable-ssl2 enable-ssl3 ;
make depend ;
make ;
make install ;
cd $SRC_ROOT_5 ;
CFLAGS="-fpic -I/usr/local/ssl/include/ -L/usr/local/ssl/lib/" ./configure --disable-shared --enable-backends=no --enable-slapd=no ;
make depend ;
make ;
make install ;
sed -i -e 's#library_dirs =#library_dirs = /usr/local/ssl/lib#' ${SRC_ROOT_0}/setup.cfg ;
sed -i -e 's#include_dirs =#include_dirs = /usr/local/ssl/include/openssl/#' ${SRC_ROOT_0}/setup.cfg ;
sed -i -e 's/libs = ldap_r/libs = lber sasl2 ldap_r ssl crypto/' ${SRC_ROOT_0}/setup.cfg ;
fi
apt:
- groff
- libsasl2-dev
- libidn11-dev
yum:
- groff
- cyrus-sasl-devel
- libidn-devel
python-lzo:
version: 1.11
src:
- http://www.oberhumer.com/opensource/lzo/download/lzo-2.10.tar.gz
insert_setuptools: true
prebuild:
wheel: cd ${SRC_ROOT_1} && CFLAGS=-fpic ./configure --prefix=${SRC_ROOT_0}/lzo --disable-shared && make install && sed -i -e 's/\["lzo"\]/\["lzo2"\]/' ${SRC_ROOT_0}/setup.py
build_args: build_ext -I lzo/include:lzo/include/lzo -L lzo/lib bdist_wheel
PyYAML:
version: 3.12
insert_setuptools: true
apt:
- libyaml-dev
yum:
- libyaml-devel
subprocess32:
version: 3.5.0
insert_setuptools: true
SQLAlchemy:
version: 1.2.2
uWSGI:
version: 2.0.17
prebuild:
all: cp ${SRC_ROOT_0}/setup.cpyext.py ${SRC_ROOT_0}/setup.py
wheel: >
[ `uname -s` != 'Darwin' ] ||
curl https://github.com/natefoo/uwsgi/commit/24c49361613fa3dbd0b61eb1a97733d48c00ff39.patch |
patch -d ${SRC_ROOT_0} -p1
apt:
- libpcre2-dev
yum:
- pcre-devel
brew:
- pcre
watchdog:
version: 0.8.3
imageset: macos-wheel
purepy_packages:
amqp:
version: 1.4.8
anyjson:
version: 0.3.3
azure-common:
version: 1.1.4
azure-nspkg:
version: 1.0.0
azure-storage:
version: 0.32.0
Babel:
version: 2.5.1
bagit:
version: 1.6.4
insert_setuptools: true
bdbag:
version: 1.2.4
Beaker:
version: 1.7.0
bioblend:
version: 0.7.0
bz2file:
version: 0.98
insert_setuptools: true
boto:
version: 2.38.0
certifi:
version: 2017.7.27.1
chardet:
version: 3.0.4
chronos-python:
version: 0.38.0
cloudauthz:
version: 0.0.2
cloudbridge:
version: 0.3.3
decorator:
version: 4.0.2
dictobj:
version: 0.3.1
docopt:
version: 0.6.2
docutils:
version: 0.12
insert_setuptools: true
ecdsa:
version: 0.13
Fabric:
version: 1.13.2
futures:
version: 3.1.1
galaxy_sequence_utils:
version: 1.0.2
httplib2:
version: 0.10.3
idna:
version: 2.6
ipaddress:
version: 1.0.18
jstree:
version: 0.4
kamaki:
version: 0.15
kombu:
version: 3.0.30
Mako:
version: 1.0.2
Markdown:
version: 2.6.3
insert_setuptools: true
nose:
version: 1.3.7
numpy-stl:
version: 1.9.1
oauth2client:
version: 4.1.2
oauthlib:
version: 1.0.3
paramiko:
version: 2.2.1
Parsley:
version: 1.3
insert_setuptools: true
Paste:
version: 2.0.2
PasteDeploy:
version: 1.5.2
pbr:
version: 2.0.0
pip:
version: 8.0.2+gx2
src:
- https://github.com/natefoo/pip/archive/03c981a2d4659d3087397dc9fd6500437998be5c.tar.gz
prebuild: sed -i -e 's/__version__ = "8\.0\.2"/__version__ = "8.0.2+gx2"/' ${SRC_ROOT}/pip/__init__.py
pulsar-galaxy-lib:
version: 0.8.0
prebuild: sed -i -e 's/DEFAULT_PULSAR_GALAXY_LIB = 0/DEFAULT_PULSAR_GALAXY_LIB = 1/' ${SRC_ROOT}/setup.py
pycparser:
version: 2.18
Pygments:
version: 2.0.2
pyjwkest:
version: 1.4.0
PyJWT:
version: 1.4.0
pykwalify:
version: 1.6.0
pyparsing:
# required by svgwrite
version: 2.1.1
python-dateutil:
version: 2.5.3
python-genomespaceclient:
version: 0.1.8
python-openid:
version: 2.2.5
insert_setuptools: true
pytz:
version: 2015.4
repoze.lru:
version: 0.7
requests:
version: 2.18.4
requests-oauthlib:
version: 0.6.1
requests-toolbelt:
version: 0.8.0
Routes:
version: 2.4.1
selenium:
version: 3.0.1
six:
version: 1.10.0
sqlalchemy-migrate:
version: 0.11.0
SQLAlchemy-Utils:
version: 0.32.19
sqlparse:
version: 0.1.16
social-auth-core:
version: 1.5.0
starforge:
version: 0.3.4
statsd:
version: 3.2.1
svgwrite:
version: 1.1.6
Tempita:
version: 0.5.3.dev0
testfixtures:
version: 4.10.0
twill:
version: 0.9.1
urllib3:
version: 1.22
wchartype:
version: 0.1
insert_setuptools: true
WebError:
version: 0.12
WebHelpers:
version: 1.3
WebOb:
version: 1.7.3
wheel:
version: 0.26.0+gx1
src:
- https://bitbucket.org/natefoo/wheel/get/795314b825f9.tar.gz
prebuild: sed -i -e 's/__version__ = "0\.26\.0"/__version__ = "0.26.0+gx1"/' ${SRC_ROOT}/wheel/__init__.py
Whoosh:
version: 2.7.4
# Whoosh:
# version: 2.4.1
# prebuild: sed -i -e 's/self\.results\.docterms\[self\.docnum\]/self.results.docterms.get(self.docnum, [])/' ${SRC_ROOT}/src/whoosh/searching.py && sed -i -e 's/versionstring()/"2.4.1+gx1"/' ${SRC_ROOT}/setup.py