artbio / metavisitor

This is the repository for the automated deployment of a Metavisitor Galaxy server.

The Metavisitor Documentation is available on https://artbio.github.io/metavisitor/

The viral Vir2 database used in Metavisitor is available for download in figshare.

Quick Start - Deploy Galaxy Metavisitor instance on a target Ubuntu machine

Tested on Ubuntu 16.04

• You need root access (be sudoer)

• You need git install (sudo apt install git -y)

• Clone locally this repository

git clone https://github.com/ARTbio/metavisitor.git

• Navigate to metavisitor directory

cd metavisitor

Deploy Metavisitor with ansible:

sh local_metavisitor_ansible_build.sh

Deploy Metavisitor with docker

sh local_metavisitor_docker_build.sh

Docker image artbio/metavisitor-2 available at https://cloud.docker.com

Run example:

docker run -d -p 80:80 -p 21:21 -p 8800:8800 \
             --privileged=true \
             -e GALAXY_CONFIG_ALLOW_USER_DATASET_PURGE=True \
             -e GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE=True \
             -e GALAXY_CONFIG_ENABLE_USER_DELETION=True \
             -e GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_MODULES=True \
             -e NGINX_GALAXY_LOCATION=/subdir \
             -v /tmp/:/tmp/ \
             -v /export:/export \
             artbio/metavisitor-2

metavisitor's Issues

Trinity tools in metavisitor-2

There are c 2 different Trinity tools in metavisitor-2 and none of them are ARTbio's

output of workflow for use case 3.1

If the output of the workflow contains normally failed (red) datasets (which I think is expected when empty inputs from oasis crash blastn), this should be clearly indicated in the documentation, otherwise users will stress.
Even if the failed datasets are silently filtered out, the user will see them during the workflow run.

@ccedmendoza please confirm, and I'll add a sentence in the documentation

edit 15 min later:

I am puzzled by the output: are you sure that the use case 3.1 is for detecting hiv, as indicated in the doc section for use case 3.1 ?

edit 15 min later.

OK this is the workflow for hiv detection, but in my test output, no trace of hiv...

still have to fix the nginx upload_store in metavisitor and probably upstream in GalaxyKickStart

More explanations to come

bowtie2 revision changeset

@ccedmendoza there is two revision changesets findable in the repo (using the search tool):

• 97d1923c8c4b
• dc1639b66f12

but only one installed with the toollist.yml.
And I think that the version installed by ansible or docker, strangely enough, is not the same. But I am not sure.