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sti-cluster
ansible_scipion
Merge requests
!2
add Xmipp and symbolic link
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Merged
add Xmipp and symbolic link
new_scipion
into
master
Overview
0
Commits
3
Pipelines
0
Changes
1
Merged
Pullyvan Krishnamoorthy
requested to merge
new_scipion
into
master
2 years ago
Overview
0
Commits
3
Pipelines
0
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1
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add Xmipp and symbolic link
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master
master (base)
and
latest version
latest version
f1b6e9ae
3 commits,
2 years ago
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tasks/main.yml
+
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Options
---
# tasks file for Scipion
-
name
:
update ubuntu
become
:
yes
package
:
update_cache
:
yes
upgrade
:
yes
##!!! depends on conda!!
-
name
:
install Scipion requirements
become
:
yes
apt
:
state
:
latest
pkg
:
-
openjdk-8-jdk
-
libopenmpi-dev
-
openmpi-bin
-
gfortran
-
libxft2
-
libxss1
-
gcc-5
-
g++-5
-
cmake
-
openjdk-8-jdk
-
libxft-dev
-
libssl-dev
-
libxext-dev
-
libxml2-dev
-
libreadline-dev
-
libquadmath0
-
libxslt1-dev
-
gcc-8
-
g++-8
-
libopenmpi-dev
-
openmpi-bin
-
libxss-dev
-
libgsl0-dev
-
libx11-dev
-
gfortran
-
libfreetype6-dev
-
scons
-
libfftw3-dev
-
libopencv-dev
-
curl
-
git
-
unzip
-
nmon
-
name
:
check scipion scipion_conf/scipion.conf exist
become
:
yes
stat
:
path
:
"
{{
scipion_conf
}}/scipion.conf"
register
:
scipion_conf_file
-
name
:
Create scipion config directory
become
:
yes
file
:
path
:
"
{{
scipion_conf
}}"
state
:
directory
mode
:
"
0755"
#when: scipion_conf.stat.exists == True
-
name
:
Scipion.conf
become
:
yes
template
:
src
:
"
templates/scipion.j2"
dest
:
"
{{
scipion_conf
}}/scipion.conf"
owner
:
root
group
:
root
mode
:
"
0755"
backup
:
yes
when
:
scipion_conf_file.stat.exists == False
-
name
:
hosts.conf
become
:
yes
template
:
src
:
"
templates/hosts.j2"
dest
:
"
{{
scipion_conf
}}/hosts.conf"
owner
:
root
group
:
root
mode
:
"
0755"
backup
:
yes
-
name
:
protocols.conf
become
:
yes
template
:
src
:
"
templates/protocols.j2"
dest
:
"
{{
scipion_conf
}}/protocols.conf"
owner
:
root
group
:
root
mode
:
"
0755"
backup
:
yes
-
name
:
create sciption folder in root directory
become
:
yes
file
:
path
:
"
{{
scipion_conf_root
}}"
state
:
directory
mode
:
"
0755"
-
name
:
Create config file scipion for root
become
:
yes
template
:
src
:
"
templates/script_scipion_root.j2"
dest
:
"
{{
scipion_conf_root
}}/scipion.conf"
owner
:
root
group
:
root
mode
:
"
0755"
backup
:
yes
-
name
:
Create scipion config all users
become
:
yes
file
:
path
:
"
{{
scipion_conf
}}"
state
:
directory
mode
:
"
0755"
#when: scipion_conf.stat.exists == False
-
name
:
Create config file scipion for all users
become
:
yes
template
:
src
:
"
templates/scipion.j2"
dest
:
"
{{
scipion_conf
}}/scipion.conf"
owner
:
root
group
:
root
mode
:
"
0755"
backup
:
yes
-
make
-
python3-pip
-
python3-mpi4py
-
name
:
Check scipion Folder
become
:
yes
stat
:
path
:
"
{{
scipion_install_destination
}}"
register
:
scipion_dir
-
name
:
Create scipion directory
become
:
yes
file
:
path
:
"
{{
scipion_install_destination
}}"
state
:
directory
mode
:
"
0755"
-
name
:
install scipion conda requirements
shell
:
source /usr/local/anaconda3/bin/activate && conda install -y -c anaconda mpi4py
args
:
executable
:
/bin/bash
# when: scipion_dir.stat.exists == False
-
name
:
"
unzip
the
binaries
of
my
software
{{
scipion_install_version
}}
into
{{
scipion_install_destination
}}"
unarchive
:
dest
:
"
{{
scipion_install_destination
}}"
src
:
"
{{
scipion_repo_base_url
}}/{{
scipion_versions[scipion_install_version]['url']
}}"
remote_src
:
yes
mode
:
"
0755"
extra_opts
:
-
-P
-
"
{{
scipion_versions[scipion_install_version]['password']
}}"
-
name
:
install scipion installer
# do not use offical pip
shell
:
source /usr/local/anaconda3/bin/activate && /usr/local/anaconda3/bin/pip install --user scipion-installer
args
:
executable
:
/bin/bash
-
name
:
Scipion installation
become
:
yes
command
:
./scipion install
-
name
:
install scipion
shell
:
source /usr/local/anaconda3/bin/activate && /usr/local/anaconda3/bin/python -m scipioninstaller -conda -noXmipp -noAsk /opt/scipion
args
:
chdir
:
"
{{
scipion_install_destination
}}/scipion-master"
executable
:
/bin/bash
#when: scipion_dir.stat.exists == False
-
name
:
check if scipion installed
become
:
yes
stat
:
path
:
"
{{
installed_path
}}"
register
:
installed_scipion_post
-
name
:
create config for scipion
shell
:
source /usr/local/anaconda3/bin/activate && /opt/scipion/scipion3 config --overwrite --unattended
args
:
executable
:
/bin/bash
-name
:
install xmipp requirements
apt
:
state
:
latest
pkg
:
-
scons
-
libfftw3-dev
-
libhdf5-dev
-
python3-numpy
-
python3-dev
-
libtiff5-dev
-
libsqlite3-dev
-
default-jdk
-
git
-
cmake
-
name
:
Install xmipp plugin
shell
:
/opt/scipion/scipion3 installp -p scipion-em-xmipp -j 12 | tee -a /tmp/xmipp_install.log
args
:
executable
:
/bin/bash
-
name
:
symbolic link for scipion
become
:
yes
file
:
src
:
"
{{
installed_path
}}"
-
name
:
Create a scipion symbolic link
ansible.builtin.file
:
src
:
/opt/scipion/scipion3
dest
:
/usr/bin/scipion
state
:
link
-
name
:
Scipion installp
become
:
yes
command
:
scipion installp -p {{ item }}
with_items
:
-
scipion-em-bionotes
-
scipion-em-bsoft
-
scipion-em-ccp4
-
scipion-em-continuousflex
-
scipion-em-cryoef
-
scipion-em-cryomethods
-
scipion-em-cryosparc2
-
scipion-em-eman2
-
scipion-em-empiar
-
scipion-em-emxlib
-
scipion-em-esrf
-
scipion-em-grigoriefflab
-
scipion-em-imagic
-
scipion-em-localrec
-
scipion-em-motioncorr
-
scipion-em-phenix
-
scipion-em-powerfit
-
scipion-em-xmipp
# - scipion-em-relion Problem GCC version ask for before 6
-
scipion-em-resmap
-
scipion-em-simple
-
scipion-em-sphire
-
scipion-em-spider
-
scipion-em-topaz
ignore_errors
:
yes
-
name
:
Scipion xmipp bundle download
become
:
yes
git
:
repo
:
"
{{
dl_urs_git
}}"
dest
:
"
{{
scipion_xmipp
}}/xmipp-bundle"
clone
:
yes
-
name
:
Scipion xmipp installation
become
:
yes
command
:
./xmipp get_devel_sources
args
:
chdir
:
"
{{
scipion_xmipp
}}/xmipp-bundle"
ignore_errors
:
yes
-
name
:
Scipion xmipp dev installation
shell
:
scipion installb xmippDev -j
8
-
name
:
Create config file scipion for profile.d
become
:
yes
template
:
src
:
"
templates/scipion_profile_d.j2"
dest
:
"
{{
scipion_profle_d
}}/config_scipion.sh"
owner
:
root
group
:
root
mode
:
a+x
backup
:
yes
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