README_genostack_galaxytest.md

galaxy install directory

https://galaxy-p2m2-192-168-100-198.vm.openstack.genouest.org/

VM configuration

Debian 10.10

ssh [email protected]

config genouest

si test-galaxy est le nom de la machine

dans /etc/hosts
127.0.0.1 test-galaxy

mount directory

• doc : https://www.genouest.org/outils/genostack/volumes.html
• /mnt/galaxy

sudo -i
lsblk -f
mkfs.ext4 /dev/vdb
mkdir /mnt/galaxy
mount /dev/vdb /mnt/galaxy

docker image

see https://github.com/bgruening/docker-galaxy-stable

cd /mnt/galaxy
git clone https://github.com/bgruening/docker-galaxy-stable.git

run

stop apache to release port 80

service apache2 stop

config (ADMIN_USER,....)

cp /mnt/galaxy/docker-galaxy-stable/compose/docker-compose.yml docker-compose.yml 
vi docker-compose.yml 
cp docker-compose.yml /mnt/galaxy/docker-galaxy-stable/compose/

run galaxy

cd /mnt/galaxy/docker-galaxy-stable/compose/
docker-compose up -d

install tool

• doc: https://galaxyproject.org/admin/tools/add-tool-tutorial/
• /mnt/galaxy/docker-galaxy-stable/compose/export/galaxy

copy tool

`sudo cp -r /home/debian/p2m2tools/galaxy/gcms2isocor /mnt/galaxy/docker-galaxy-stable/compose/export/galaxy/tools/

add tool menu

if tool_conf.xml exist : cp tool_conf.xml /mnt/galaxy/docker-galaxy-stable/compose/export/galaxy/config/

or create /mnt/galaxy/docker-galaxy-stable/compose/export/galaxy/config/tool_conf.xml

<?xml version="1.0"?>
<toolbox>
  <section name="Metabolomics" id="metabolomics">
        <tool file="gcms2isocor/gcms2isocor.xml" />
  </section>

 <section name="Metabolomics" id="metabolomics">
        <tool file="openlabcds2csv/openlabcds2csv.xml" />
 </section>


 <section name="Metabolomics" id="metabolomics">
     <tool file="masslynx2isocor/masslynx2isocor.xml" />
 </section>

</toolbox>