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|
# @copyright 2016-2021 Clarity Genomics BVBA
# @copyright 2012-2016 Bonsai Bioinformatics Research Group
# @copyright 2014-2016 Knight Lab, Department of Pediatrics, UCSD, La Jolla
#
# SortMeRNA - next-generation reads filter for metatranscriptomic or total RNA
# This is a free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# SortMeRNA is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with SortMeRNA. If not, see <http://www.gnu.org/licenses/>.
#
# contributors: Jenya Kopylova jenya.kopylov@gmail.com
# Laurent Noé laurent.noe@lifl.fr
# Pierre Pericard pierre.pericard@lifl.fr
# Daniel McDonald wasade@gmail.com
# Mikaël Salson mikael.salson@lifl.fr
# Hélène Touzet helene.touzet@lifl.fr
# Rob Knight robknight@ucsd.edu
#
# file: env.jinja
# created: Oct 28, 2019 Mon
#
# sample configuration
#
{%- set CMAKE_VER = '3.20.1' %} # pre: 3.16.8 20210423
{%- set GIT_VER_MAJ = '2.24.0' %}
{%- set GIT_VER_MIN = '2.24.0.2' %}
{%- set ROCKSDB_VER = 'v7.1.1' %} # Optional. Default: Git master head current (20210423): v6.8.1 6.4.6
{%- set ENV = ENV or 'WIN' %} # name of environment: WIN | WSL | LNX_AWS | LNX_TRAVIS
{%- set BIN_USER_WIN = UHOME~'/a1/apps' %}
{%- set CODE_USER_WIN = UHOME~'/a1/code' %}
{%- set ZLIB_LINK_WIN_REL_T1 = 'zlibstatic.lib' %}
{%- set ZLIB_LINK_WIN_DBG_T1 = 'zlibstaticd.lib' %}
{%- set LIB_DIR_WIN = UHOME~'/a1/libs' %}
# WINHOME - set using command line option 'winhome' and passed here for Jinja parser to process
env.list:
- WIN
- WSL
- LIN # generic Linux
- LIN_Ubuntu_2204
- LNX_VBox_Ubuntu_1604
- LNX_VBox_Ubuntu_1804
- LNX_VBox_Centos_77
- LNX_AWS
pkg.list: # packages that can be built/installed using this 'env.jinja' configuration
- sortmerna
- zlib
- rocksdb
# - rapidjson
- conda
- all
env.config:
- env: # list of environments using a particular setup
- LIN
- LIN_Ubuntu_2204
packages: # list of packages required
- git
- conda
- gcc
- cmake
- make
- binutils
#- ninja-build
conda.packages: # list of conda packages required
- pyyaml
- jinja2
- requests
- scikit-bio
#
# optional variables
#
env: {{ENV}}
DATA_DIR:
WIN: {{ UHOME }}/a1/data
WSL: {{ WINHOME }}/a1/data
LNX_VBox_Ubuntu_1604: /media/sf_a01_data
LNX_VBox_Ubuntu_1804: /media/sf_a01_data
LNX_VBox_Centos_77: /media/sf_a01_data
LNX_AWS: /var/a1/data
LIN: {{UHOME}}/a1/data
LIN_Ubuntu_2204: {{UHOME}}/a1/data
LIB_DIR:
WIN: {{ UHOME }}/a1/libs # Optional. 3rd party libraries location. Default: SMR_SRC/3rdparty/
WSL: {{ WINHOME }}/a1/libs
LNX_AWS: /opts # optional. Default: $HOME
LNX_VBox_Ubuntu_1604: /media/sf_a01_libs
LNX_VBox_Ubuntu_1804: /media/sf_a01_libs
LNX_VBox_Centos_77: /media/sf_a01_libs
LIN: {{UHOME}}/a1/code
WRK_DIR:
WIN: {{ UHOME }}/a1/data/sortmerna/run
WSL:
LNX_VBox_Ubuntu_1804:
LNX_AWS: /var/sortmerna/run
LIN: {{UHOME}}/a1/data/sortmerna/run
#
# ==== Libraries ====
#
sortmerna:
url: https://github.com/biocore/sortmerna.git
ver:
src:
WIN: {{ CODE_USER_WIN }}/sortmerna # Default: $HOME/sortmerna
WSL: {{WINHOME}}/a1/code/sortmerna
LNX_AWS: /opts/sortmerna
LNX_TRAVIS: /home/travis/build/biocore/sortmerna
LNX_VBox_Ubuntu_1604: /media/sf_a01_code/sortmerna
LNX_VBox_Ubuntu_1804: /media/sf_a01_code/sortmerna
LNX_VBox_Centos_77: /media/sf_a01_code/sortmerna
LIN_Ubuntu_2204: {{UHOME}}/a1/code/sortmerna
LIN: {{UHOME}}/a1/code/sortmerna
build:
WIN: # Default: SMR_SRC/build
WSL: {{UHOME}}/sortmerna/build
LNX_AWS: /opts/sortmerna/build
LNX_VBox_Ubuntu_1604: {{UHOME}}/sortmerna/build
LNX_VBox_Ubuntu_1804: {{UHOME}}/sortmerna/build
LNX_VBox_Centos_77: {{UHOME}}/sortmerna/build
LIN: {{UHOME}}/a1/code/sortmerna/build
LIN_Ubuntu_2204: {{UHOME}}/a1/code/sortmerna/build
dist:
WIN: # Default: SMR_SRC/dist
WSL: {{UHOME}}/sortmerna/dist
LNX_AWS: /opts/sortmerna/dist
LNX_VBox_Ubuntu_1604: {{UHOME}}/sortmerna/dist
LNX_VBox_Ubuntu_1804: {{UHOME}}/sortmerna/dist
LNX_VBox_Centos_77: {{UHOME}}/sortmerna/dist
LIN: {{UHOME}}/a1/code/sortmerna/dist
LIN_Ubuntu_2204: {{UHOME}}/a1/code/sortmerna/dist
bin:
LNX_AWS: /opts/sortmerna/bin
# build related info
build_type: release
link:
WIN:
t1:
name: RocksDB-static + Zlib-static + Runtime-dynamic-multithreaded
zlib: t1 # zlib library linkage type
rocksdb: t3 # rocksdb library linkage type
LNX:
t1:
name: RocksDB-static + Zlib-static + Runtime-static
zlib: t1 # zlib library linkage type
rocksdb: t3 # rocksdb library linkage type
LIN:
t1:
name: RocksDB-static + Zlib-static + Runtime-static
zlib: t1 # zlib library linkage type
rocksdb: t3 # rocksdb library linkage type
dirent:
url: https://github.com/tronkko/dirent
src:
WIN: {{ LIB_DIR_WIN }}/dirent
build:
dist:
zlib:
url: https://github.com/madler/zlib.git
src:
WIN: {{ LIB_DIR_WIN }}/zlib # LIB_DIR/zlib
WSL: {{ WINHOME }}/a1/libs/zlib #
LNX_AWS: /opts/zlib
LNX_TRAVIS: #
LNX_VBox_Ubuntu_1604: /media/sf_a01_libs/zlib
LNX_VBox_Ubuntu_1804: /media/sf_a01_libs/zlib
LNX_VBox_Centos_77: /media/sf_a01_libs/zlib
LIN: {{UHOME}}/a1/code/zlib
build:
LNX_AWS: /opts/zlib/build # optional. Default: $HOME/zlib/build
LNX_VBox_Ubuntu_1604: {{UHOME}}/zlib/build
LNX_VBox_Ubuntu_1804: {{UHOME}}/zlib/build
LNX_VBox_Centos_77: {{UHOME}}/zlib/build
LIN: {{UHOME}}/a1/code/zlib/build
dist:
WSL: {{UHOME}}/zlib/dist
LNX_AWS: /opts/zlib/dist # optional. Default: $HOME/zlib/dist
LNX_VBox_Ubuntu_1604: {{UHOME}}/zlib/dist
LNX_VBox_Ubuntu_1804: {{UHOME}}/zlib/dist
LNX_VBox_Centos_77: {{UHOME}}/zlib/dist
LIN: {{UHOME}}/a1/code/zlib/dist
# build related info
build_type: release
link:
WIN:
t1:
type: MD/MDd # multi-threaded DLL runtime lib (default)
dir: t1 # added to the distribution location path i.e. $ZLIB_SRC/dist/t1/
release: {{ ZLIB_LINK_WIN_REL_T1 }}
debug: {{ ZLIB_LINK_WIN_DBG_T1 }}
t2:
type: MT/MTd # mutli-threaded Static runtime lib. Needs either CMakeLists modification, or command line options.
dir: t2
rocksdb:
info: build from GitHub sources
url: https://github.com/facebook/rocksdb.git
ver: {{ ROCKSDB_VER }}
src: # Default: LIB_DIR/rocksdb
WIN: {{ LIB_DIR_WIN }}/rocksdb
LNX_AWS: /opts/rocksdb # optional. Default: $HOME/rocksdb
LNX_VBox_Ubuntu_1604: /media/sf_a01_libs/rocksdb
LNX_VBox_Ubuntu_1804: /media/sf_a01_libs/rocksdb
LNX_VBox_Centos_77: /media/sf_a01_libs/rocksdb
LIN: {{UHOME}}/a1/code/rocksdb
build:
LNX_AWS: /opts/build # optional. Default: $HOME/rocksdb/build
LNX_VBox_Ubuntu_1604: /home/biocodz/rocksdb/build
LNX_VBox_Ubuntu_1804: /home/biocodz/rocksdb/build
LNX_VBox_Centos_77: /home/biocodz/rocksdb/build
LIN: {{UHOME}}/a1/code/rocksdb/build
dist:
WSL: {{UHOME}}/rocksdb/dist
LNX_AWS: /opts/dist # optional. Default: $HOME/rocksdb/dist
LNX_VBox_Ubuntu_1604: {{UHOME}}/rocksdb/dist
LNX_VBox_Ubuntu_1804: {{UHOME}}/rocksdb/dist
LNX_VBox_Centos_77: {{UHOME}}/rocksdb/dist
LIN: {{UHOME}}/a1/code/rocksdb/dist
# build related info
build_type: release
# linkage types
link:
WIN:
t1:
# cmake flags
WITH_MD_LIBRARY: 1
WITH_XPRESS: 1
WITH_ZLIB: 1
t2:
WITH_MD_LIBRARY: 1
WITH_XPRESS: 1
WITH_ZLIB: 1
t3: # default
name: RocksDB:static + ZLib:static + Runtime:dynamic:multithreaded
WITH_MD_LIBRARY: 1
WITH_XPRESS: 1
WITH_ZLIB: 1
ZLIB_LIB_DEBUG: {{ ZLIB_LINK_WIN_DBG_T1 }}
ZLIB_LIB_RELEASE: {{ ZLIB_LINK_WIN_REL_T1 }}
PORTABLE: 0
OPTDBG: 0
WITH_RUNTIME_DEBUG: 0
WITH_TESTS: 0
WITH_TOOLS: 0
LNX:
#rapidjson:
# url: https://github.com/Tencent/rapidjson
# src:
# WIN: {{ LIB_DIR_WIN }}/rapidjson
# LNX_AWS: /opts/rapidjson # optional. Default: $HOME/rapidjson
# LNX_VBox_Ubuntu_1604: /media/sf_a01_libs/rapidjson
# LNX_VBox_Ubuntu_1804: /media/sf_a01_libs/rapidjson # Default: LIB_DIR/rapidjson
# LNX_VBox_Centos_77: /media/sf_a01_libs/rapidjson
# LIN: {{UHOME}}/a1/code/rapidjson
# build:
# LNX_AWS: /opts/rapidjson/build # optional. Default: $HOME/rapidjson/build
# LNX_VBox_Ubuntu_1604: /home/biocodz/rapidjson/build
# LNX_VBox_Ubuntu_1804: /home/biocodz/rapidjson/build
# LNX_VBox_Centos_77: /home/biocodz/rapidjson/build
# LIN: {{UHOME}}/a1/code/rapidjson/build
# dist:
# WSL: {{UHOME}}/rapidjson/dist
# LNX_AWS: /opts/rapidjson/dist # optional. Default: $HOME/rapidjson/dist
# LNX_VBox_Ubuntu_1604: /home/biocodz/rapidjson/dist
# LNX_VBox_Ubuntu_1804: /home/biocodz/rapidjson/dist
# LNX_VBox_Centos_77: /home/biocodz/rapidjson/dist
# LIN: {{UHOME}}/a1/code/rapidjson/dist
concurrentqueue:
url: https://github.com/cameron314/concurrentqueue
src:
WIN: {{ LIB_DIR_WIN }}/concurrentqueue
#LNX: UHOME/concurrentqueu/ # default
LNX_AWS: /opts/concurrentqueue
LNX_VBox_Ubuntu_1604: /media/sf_a01_libs/concurrentqueue
LNX_VBox_Ubuntu_1804: /media/sf_a01_libs/concurrentqueue
LNX_VBox_Centos_77: /media/sf_a01_libs/concurrentqueue
LIN: {{UHOME}}/a1/code/concurrentqueue
#
# ==== Tools ====
#
cmake:
ver: {{CMAKE_VER}}
url:
WIN: https://github.com/Kitware/CMake/releases/download/v{{CMAKE_VER}}/cmake-{{CMAKE_VER}}-win64-x64.zip
LNX: https://github.com/Kitware/CMake/releases/download/v{{CMAKE_VER}}/cmake-{{CMAKE_VER}}-Linux-x86_64.tar.gz
root:
WIN: # default: User home
WSL:
LNX_AWS: /opts # default: User home
LNX_TRAVIS: # default $HOME
generator:
WIN: Visual Studio 17 2022 # Visual Studio 16 2019 | Ninja
WSL: Unix Makefiles
LNX: Unix Makefiles
LIN: Unix Makefiles
home:
WIN: {{ BIN_USER_WIN }}/cmake-{{CMAKE_VER}}-win64-x64
LNX_AWS: /opts/cmake-{{CMAKE_VER}}-Linux-x86_64
LNX_VBox_Ubuntu_1604: {{UHOME}}/cmake-{{CMAKE_VER}}-Linux-x86_64
LNX_VBox_Ubuntu_1804: {{UHOME}}/cmake-{{CMAKE_VER}}-Linux-x86_64
LNX_VBox_Centos_77: {{UHOME}}/cmake-{{CMAKE_VER}}-Linux-x86_64
conda:
url:
WIN:
LNX: 'http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh'
root:
WIN:
LNX_TRAVIS: # default HOME
git:
url:
WIN: https://github.com/git-for-windows/git/releases/download/v{{ GIT_VER_MAJ }}.windows.2/PortableGit-{{ GIT_VER_MIN }}-64-bit.7z.exe
root: # default: User home
home:
WIN: {{ BIN_USER_WIN }}/PortableGit-{{ GIT_VER_MIN }}-64
OSX:
SMR_SRC:
DATA_DIR:
# Optional ->
build:
dist:
LIB_DIR:
DIRENT_SRC:
ZLIB_SRC:
ROCKSDB_SRC:
RAPID_SRC:
|
