backofenlab/graphclust-2

A pipeline for structural clustering of RNA secondary structures

GraphClust2

GraphClust2 is a workflow for scalable clustering of RNAs based on sequence and secondary structures feature. GraphClust2 is implemented within the Galaxy framework and consists a set of integrated Galaxy tools and flavors of the linear-time clustering workflow.

Table of Contents

• GraphClust2
• Table of Contents
• Availability
  • GraphClust2 on European Galaxy Server
  • GraphClust2 Docker 🐳 Image
    • Installation and Setup
      • Requirements
    • Running the docker instance
      • Using graphic interface (Windows/MacOS)
  • Installation on a Galaxy instance
    • Setup support
  • Demo instance
• Usage - How to run GraphClust2
  • Browser access to the server
    • Public server
    • Docker instance
    • Video tutorial
    • Interactive tours
    • Import additional workflows
    • Workflow flavors
      • Workflows on the running server
  • command line support (beta)
  • Frequently Asked Questions
• Workflow overview
  • Input
  • Output
• Support & Bug Reports
• References

Availability

GraphClust2 on European Galaxy Server

GraphClust2 is accessible on European Galaxy server at:

• https://graphclust.usegalaxy.eu

GraphClust2 Docker 🐳 Image

It is also possible to run GraphClust2 as a stand-alone solution using a Docker container that is a pre-configured flavor of the official Galaxy Docker image. This Docker image is a flavor of the Galaxy Docker image customized for GraphClust2 tools, tutorial interactive tours and workflows.

Installation and Setup

Requirements

For running GraphClust2 locally, the Docker client is required. Docker supports the three major desktop operating systems Linux, Windows and Mac OSX. Please refer to thw Docker installation guideline for details.

A GUI client can also be used for Windows and Mac operation systems. Please follow the graphical instructions for using Kitematic client here.

Hardware requirements:

• Minimum 8GB memory
• Minimum 20GB free disk storage space, 100GB is recommended.

Supported operating systems

GraphClust2 has been tested on these operating systems:

• Windows : 10 using Kitematic
• MacOSx: 10.1x or higher using Kitematic
• Linux: Kernel 4.2 or higher, preferably with aufs support (see FAQ)

Running the docker instance

From the command line:

docker run -i -t -p 8080:80 backofenlab/docker-galaxy-graphclust

For details about the docker commands please check the official guide here. Galaxy specific run options and configuration supports for computation grid systems are detailed in the Galaxy Docker repository.

Using graphic interface (Windows/MacOS)

Please check this step-by-step guide.

Installation on a Galaxy instance

GraphClust2 can be integrated into any available Galaxy server. All the GraphClust2 tools and workflows needed to run the GraphClust pipeline are listed in workflows and tools-list.

Setup support

In case you encountered problems please use the recommended settings, check the FAQs or contact us via Issues section of the repository.

Demo instance

A running demo instance of GraphClust2 is available at http://192.52.32.222:8080/. Please note that this instance is simply a Cloud instance of the provided Docker container, intended for rapid inspections and demonstration purposes. The computation capacity is limited and currently it is not planned to have a long-time availability. We recommend to follow instructions above. Please contact us if you prefer to keep this service available.

Usage - How to run GraphClust2

Browser access to the server

Public server

Please register on our European Galaxy server https://usegalaxy.eu and use your authentication information to access the customized sub-domain [https://graphclust.usegalaxy.eu]. Guides and tutorial are available in the server welcome home page.

Docker instance

After running the Galaxy docker, a web server is established under the host IP/URL and designated port (default 8080).

• Inside your browser goto IP/URL:PORT
• Following same settings as previous step
  • In the same (local) computer: http://localhost:8080/
  • In other systems in the network: http://HOSTIP:8080

Video tutorial

You might find this Youtube tutorial helpful to get a visually comprehensive introduction on setting-up and running GraphClust2.

Interactive tours

Interactive Tours are available for Galaxy and GraphClust2. To run the tours please on top panel go to Help→Interactive Tours and click on one of the tours prefixed GraphClust. You can check the other tours for a more general introduction to the Galaxy interface.

Import additional workflows

To import or upload additional workflow flavors (e.g. from extra-workflows directory), on the top panel go to Workflow menu. On top right side of the screen click on "Upload or import workflow" button. You can either upload workflow from your local system or by providing the URL of the workflow. Log in is necessary to access into the workflow menu. The docker galaxy instance has a pre-configured easy! info that can be found by following the interactive tour. You can download workflows from the following links

Workflow flavors

The pre-configured flavors of GraphClust2 are provided and described inside the workflows directory

Workflows on the running server

Below workflows can be directly accessed on the public server:

• MotifFinder: GraphClust-MotifFinder
• Workflow main: GraphClust_1r
• Workflow main, preconfigured for two rounds : GraphClust_2r

command line support (beta)

Galaxy service is accessible via the Galaxy project bioblend API library. In the future we plan to provide a full integration of bioblend API for GraphClust2. Currently a beta support for running GraphClust2 via the CLI is available. The wrapper and setup template is available inside CLI-workflow-executor directory.

Frequently Asked Questions

Workflow overview

The pipeline for clustering RNA sequences and structured motif discovery is a multi-step pipeline. Overall it consists of three major phases: a) sequence based pre-clustering b) encoding predicted RNA structures as graph features c) iterative fast candidate clustering then refinement

Below is a coarse-grained correspondence list of GraphClust2 tool names with each step:

Stage	Galaxy Tool Name	Description
1	Preprocessing	Input preprocessing (fragmentation)
2	fasta_to_gspan	Generation of structures via RNAshapes and conversion into graphs
3	NSPDK_sparseVect	Generation of graph features via NSPDK
4	NSPDK_candidateClusters	min-hash based clustering of all feature vectors, output top dense candidate clusters
5	PGMA_locarna,locarna, CMfinder	Locarna based clustering of each candidate cluster, all-vs-all pairwise alignments, create multiple alignments along guide tree, select best subtree, and refine alignment.
6	Build covariance models	create candidate model
7	Search covariance models	Scan full input sequences with Infernal's cmsearch to find missing cluster members
8,9	Report results and conservation evaluations	Collect final clusters and create example alignments of top cluster members

Input

The input to the workflow is a set of putative RNA sequences in FASTA format. Inside the data directory you can find examples of the input format. The labeled datasets are based on Rfam annotation that are labeled with the associated RNA family.

Output

The output contains the predicted clusters, where similar putative input RNA sequences form a cluster. Additionally overall status of the clusters and the matching of cluster elements is reported for each cluster.

Support & Bug Reports

You can file a github issue or find our contact information in the lab page.

References

The manuscript is currently under prepration/revision. If you find this resource useful, please cite the zenodo DOI of the repo or contact us.

• Miladi, Milad, Eteri Sokhoyan, Torsten Houwaart, Steffen Heyne, Fabrizio Costa, Bjoern Gruening, and Rolf Backofen. "GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering." GigaScience, Volume 8, Issue 12, December 2019, giz150. doi: https://doi.org/10.1093/gigascience/giz150
• Milad Miladi, Björn Grüning, & Eteri Sokhoyan. BackofenLab/GraphClust-2: Zenodo. http://doi.org/10.5281/zenodo.1135094
• GraphClust-1 methodology (S. Heyne, F. Costa, D. Rose, R. Backofen; GraphClust: alignment-free structural clustering of local RNA secondary structures; Bioinformatics, 2012) available at http://www.bioinf.uni-freiburg.de/Software/GraphClust/

graphclust-2's Issues

Upgrade to 17.09 fails

Pinning Docker file to 17.07 causes the test/build to fail. Probably due to the developments in docker-galaxy-stable scripts for handling the authentication and/or installing the tools..

https://travis-ci.org/BackofenLab/docker-galaxy-graphclust/builds/299705075#L1467

rnafold and rnafold-SHAPE workflows can be merged to avoid redundancy

Extend locarna wrapper parameters

locARNAGraphClust.pl has a set of fixed parameters for calling LocARNA (OPTS_locarna_model, OPTS_locarna_maligs,..) that should be not set by default and be exposed to the user.

OPTS_locarna_maligs           -p 0.001 --max-diff-am 50 --tau 50 --alifold-consensus-dp --max-diff 100
OPTS_locarna_model            -p 0.001 --max-diff-am 50 --tau 50 --alifold-consensus-dp
OPTS_locarna_p_model          -p 0.001 --max-diff-am 50 --tau 50  --struct-weight 160 --plfold-span 150 --plfold-winsize 200 --temperature 180 --mea-beta 400 --consistency-transformation

Optimizing Parameters for Larger Motif Window

Hello:

Trying to run motiffinder on larger RNA windows ~150 - 250nt. We are getting fail states at the Structure-to-GSPAN step and are unable to generate clusters.

Any advice on what parameters to fine-tune as you open up the window?

Galaxy workflows and datasets

• We need to include a few workflows as case-study.
• datasets needs to be included

nspdk_candidate_clusters non data-collection svector

nspdk_candidate_clusters script currently only work with data-collection format for the input data-svector. User must be prohibited from passing non-data-collection svector.

Parallel mode for NSPDK vectorizer

Probably there is a multithreaded mode for NSPDK vectorizer, that we can enable to speedup

Testing the tools and workflows

Please add all things that you encounter to this issue.

Improve wrapper namings

• premlocarna -> ?
• locarna_best_subtree -> locarna_graphclust
• Cmfinder_v0 -> cmfinder
• Report_results -> cluster_collection_report

nspdk_candidate_clusters multi round _m output can be merged

nspdk_candidate_clusters uses _m suffixed output pin for multi rounds, while for the first round default pins are used. These two output types are mutually exclusive and can be merged to avoid confusion for connection multiround outputs.

GraphClust-2 on RNA-seq data?

Mine is a question and not an issue, I am very new to this area.
I got a rich deepgen fastq data set (coming from rna-seq data) of an organism we know the reference genome but nothing about non coding RNA.
I easily got a bam file out of it after quality control and alignment...
is there any way I could use graph-clust-2 to detect and classify non coding RNA in the whole genome starting from the bam file?
Will it make sense for my purpose to use your software?
Thank you very much!

RNA type identification after graphclust analysis

I started NSPDK_sparseVect process on Galaxy and is at its third running day. I am not sure if this is normal.
Plus its input GSPAN groups file, when locally downloaded, looks like a corrupted zip file.
My email is [email protected].

Readme file needs to be updated

• more installation guidance
• aim, motivation, ref to the graphclust paper

Change welcome page and add more help text.

Cascadable workflow needed

To have clustering extendable to multiple iterations we need to either:

• Make sub-Workflows running
  Or
• make a workflow of single iteration such that byinvoking it multiple times in a cascaded manner(output of previous run as the input of new run) we achieve multiple iteration runs

First option works only if sub workflows be functional in galaxy release.
With the second option we know the basic ingredients exist.

Cmsearch output threshold

Cmsearch step has two types of thresholds: Reporting & Inclusion
The reporting threshold is so high by default (E-val 10) and should not be changed if it used as the output for the next step.
@eteriSokhoyan Pls have look at this.

Dropdown list is not statically updated

Consider a scenario where a wrapper/workflow is already opened and some data processing is running. For a newly generated data, it is not shown inside the dropdown list of opened wrapper input section. The user have to reopen the wrapper again to see new data in the dropdown list.

This issue is described here:
bgruening/docker-galaxy-stable#279

However apparently it does happen for galaxy-graphclust and does not affect docker-galaxy-stable.

Documentation and tour on how to import a workflow

R-scape output

Hi Eteri,
Do you include all R-scape output (all pdf and svg figures, text output) to the Results.zip directory?

conda issue for dependencies

Recent docker builds are missing binary files for at least two dependencies (r-scape and graphicsmagic) in the conda environment.

root@d78eb3aeff9e:/export/tool_deps/_conda/envs/mulled-v1-7cc55d4faf2226e75728e1595b08d0f7cdf9df9e42ca7b72736337c5adc8f30b/bin# ls gm
ls: cannot access gm: No such file or directory

The tools are reported to be installed in the admin section:
https://files.gitter.im/mmiladi/naMU/Screenshot-from-2017-11-08-19-47-54.png

The docker built reports some warnings that might be related, but unfort I couldn't trace it
https://hub.docker.com/r/backofenlab/docker-galaxy-graphclust/builds/bgm632if4ep6ooflhhnjxa5/

From the docker log:

..
Removing intermediate container 78e8d6d4eb41

Step 7/12 : ADD ./tours/* $GALAXY_ROOT/config/plugins/tours/

 ---> cb571ff63108

Removing intermediate container 1c7e2be5f860

Step 8/12 : ADD library_data.yaml $GALAXY_ROOT/library_data.yaml

 ---> fefc990320b4

Removing intermediate container 37ad2222c8dc

Step 9/12 : ADD ./workflows/* $GALAXY_ROOT/workflows/

 ---> 00edc96b285e

Removing intermediate container 82208dbb89af

Step 10/12 : RUN startup_lite &&     sleep 30 &&     . $GALAXY_VIRTUAL_ENV/bin/activate &&     workflow-install --workflow_path $GALAXY_ROOT/workflows/ -g http://localhost:8080 -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD &&     setup-data-libraries -i $GALAXY_ROOT/library_data.yaml -g http://localhost:8080 -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD

 ---> Running in abe7b492197d

 * Starting PostgreSQL 9.3 database server

   ...done.

Activating virtualenv at /galaxy_venv

�[91mThe directory '/home/galaxy/.cache/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
�[0m
�[91mThe directory '/home/galaxy/.cache/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
�[0m
Requirement already satisfied: pip>=8.1 in /galaxy_venv/lib/python2.7/site-packages

�[91m/galaxy_venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:318: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#snimissingwarning.
  SNIMissingWarning
/galaxy_venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#insecureplatformwarning.
  InsecurePlatformWarning
�[0m
Activating virtualenv at /galaxy_venv

galaxy.tools.deps DEBUG 2017-11-09 10:23:40,830 Unable to find config file './dependency_resolvers_conf.xml'

 ---> bf2b502747a0

Removing intermediate container abe7b492197d

Step 11/12 : ADD workflow_early.png $GALAXY_CONFIG_DIR/web/welcome_image.png

..

Gspan group option

Gspan group option to split and distribute the computation might not work under certain conditions and needs proper testing

Galaxy 18.05 docker

Running the 18.05 branch on Ubuntu 18.04 reports error:

Starting slurmd
Creating admin user [email protected] with key admin and password admin if not existing
Traceback (most recent call last):
  File "/usr/local/bin/create_galaxy_user.py", line 60, in <module>
    add_user(sa_session, security_agent, options.user, options.password, key=options.key, username=options.username)
  File "/usr/local/bin/create_galaxy_user.py", line 36, in add_user
    sa_session.flush()
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/scoping.py", line 153, in do
    return getattr(self.registry(), name)(*args, **kwargs)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2254, in flush
    self._flush(objects)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2380, in _flush
    transaction.rollback(_capture_exception=True)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 66, in __exit__
    compat.reraise(exc_type, exc_value, exc_tb)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2344, in _flush
    flush_context.execute()
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 391, in execute
    rec.execute(self)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 556, in execute
    uow
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 181, in save_obj
    mapper, table, insert)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 866, in _emit_insert_statements
    execute(statement, params)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute
    return meth(self, multiparams, params)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 269, in _execute_on_connection
    return connection._execute_clauseelement(self, multiparams, params)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1060, in _execute_clauseelement
    compiled_sql, distilled_params
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context
    context)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception
    exc_info
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause
    reraise(type(exception), exception, tb=exc_tb, cause=cause)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context
    context)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.IntegrityError: (psycopg2.IntegrityError) duplicate key value violates unique constraint "ix_api_keys_key"
DETAIL:  Key (key)=(admin) already exists.
 [SQL: 'INSERT INTO api_keys (create_time, user_id, key) VALUES (%(create_time)s, %(user_id)s, %(key)s) RETURNING api_keys.id'] [parameters: {'create_time': datetime.datetime(2018, 10, 12, 13, 31, 44, 786901), '
user_id': 2, 'key': 'admin'}] (Background on this error at: http://sqlalche.me/e/gkpj)
tail: unrecognized file system type 0x794c7630 for ‘/home/galaxy/logs/reports.log’. please report this to [email protected]. reverting to polling
tail: unrecognized file system type 0x794c7630 for ‘/home/galaxy/logs/slurmctld.log’. please report this to [email protected]. reverting to polling
==> /home/galaxy/logs/reports.log <==
galaxy.web.framework.base DEBUG 2018-10-12 13:31:18,273 Enabling 'tools' controller, class: Tools
galaxy.web.framework.base DEBUG 2018-10-12 13:31:18,273 Enabling 'root' controller, class: Report
galaxy.web.framework.base DEBUG 2018-10-12 13:31:18,274 Enabling 'home' controller, class: HomePage
galaxy.webapps.util DEBUG 2018-10-12 13:31:18,276 Enabling 'paste.httpexceptions' middleware
galaxy.webapps.util DEBUG 2018-10-12 13:31:18,276 Enabling 'RecursiveMiddleware' middleware
galaxy.webapps.util DEBUG 2018-10-12 13:31:18,280 Enabling 'ErrorMiddleware' middleware
galaxy.webapps.util DEBUG 2018-10-12 13:31:18,280 Enabling 'TransLogger' middleware
galaxy.webapps.util DEBUG 2018-10-12 13:31:18,281 Enabling 'XForwardedHostMiddleware' middleware
Starting server in PID 306.
serving on http://127.0.0.1:9001

==> /home/galaxy/logs/slurmctld.log <==
[2018-10-12T13:31:43.106] error: Could not open trigger state file /tmp/slurm/trigger_state: No such file or directory
[2018-10-12T13:31:43.106] error: NOTE: Trying backup state save file. Triggers may be lost!
[2018-10-12T13:31:43.106] No trigger state file (/tmp/slurm/trigger_state.old) to recover
[2018-10-12T13:31:43.106] error: Incomplete trigger data checkpoint file
[2018-10-12T13:31:43.106] read_slurm_conf: backup_controller not specified.
[2018-10-12T13:31:43.106] Reinitializing job accounting state
[2018-10-12T13:31:43.106] cons_res: select_p_reconfigure
[2018-10-12T13:31:43.106] cons_res: select_p_node_init
[2018-10-12T13:31:43.106] cons_res: preparing for 1 partitions
[2018-10-12T13:31:43.106] Running as primary controller

==> /home/galaxy/logs/slurmd.log <==
[2018-10-12T13:31:43.102] CPU frequency setting not configured for this node
[2018-10-12T13:31:43.103] slurmd version 2.6.5 started
[2018-10-12T13:31:43.104] slurmd started on Fri, 12 Oct 2018 13:31:43 +0000
[2018-10-12T13:31:43.104] CPUs=8 Boards=1 Sockets=8 Cores=1 Threads=1 Memory=16039 TmpDisk=99067 Uptime=4509

==> /home/galaxy/logs/uwsgi.log <==
galaxy.web.stack DEBUG 2018-10-12 13:31:18,330 [p:339,w:2,m:0] [MainThread] Calling postfork function: <function postfork_setup at 0x7fde2b6eab18>
galaxy.web.stack DEBUG 2018-10-12 13:31:18,330 [p:336,w:1,m:0] [MainThread] Calling postfork function: <function register at 0x7fde375eda28>
galaxy.queue_worker INFO 2018-10-12 13:31:18,330 [p:339,w:2,m:0] [MainThread] Binding and starting galaxy control worker for main.web.2
galaxy.web.stack DEBUG 2018-10-12 13:31:18,331 [p:336,w:1,m:0] [MainThread] Calling postfork function: <function postfork_setup at 0x7fde2b6eab18>
galaxy.queue_worker INFO 2018-10-12 13:31:18,331 [p:336,w:1,m:0] [MainThread] Binding and starting galaxy control worker for main.web.1
galaxy.web.stack INFO 2018-10-12 13:31:18,339 [p:336,w:1,m:0] [MainThread] Galaxy server instance 'main.web.1' is running
Starting server in PID 206.
serving on http://127.0.0.1:8080
serving on uwsgi://127.0.0.1:4001
galaxy.web.stack INFO 2018-10-12 13:31:18,343 [p:339,w:2,m:0] [MainThread] Galaxy server instance 'main.web.2' is running
tail: unrecognized file system type 0x794c7630 for ‘/home/galaxy/logs/slurmd.log’. please report this to [email protected]. reverting to polling
tail: unrecognized file system type 0x794c7630 for ‘/home/galaxy/logs/uwsgi.log’. please report this to [email protected]. reverting to polling

Improving readme

Please write down suggestion for enriching the readme and instructions here

Locarna Free-endgaps option for collect results

Hi @eteriSokhoyan , could you please think of adding free-endgaps option to locarna options of the collect results? You can get the template from original locarna package. or even better integrate locarna wrapper inside/after collect-results

With recent updates Workflows are not automatically added during docker build

Add e-value to CLUSTERS table

Master 'dev/ version needs more testing

With the lastest version of the docker with tag 'dev' in cases the workflow fails on cmsearch step. @eteriSokhoyan I think you were right something is getting incompatible. Please keep this issue in highest priority to check and resolve.

Docker daily builds and latest tag

Because of some broken pipeline runs, It would be better to assign docker latest tag to latest released github version, not to the master branch. In this case it is also crucial to stop daily rebuilding of released stable docker container.
@bgruening Which entity triggers the daily builds of the tags? How can I stop the daily automatic rebuilds :-D?

cmbuild/cmcalibrate multi-threading

cmcalibrate is a very time consuming process, which is an integrated part of cmbuild galaxy wrapper. Multi-threading is critically demanded for running the calibration. Currently 2 slots (--cpu "\${GALAXY_SLOTS:-2}") are hard-coded in the wrapper: https://github.com/bgruening/galaxytools/blob/master/tools/rna_tools/infernal/cmbuild.xml#L90

For an unknown reason the galaxy docker instance only assigns one process to the task (run time process info: --cpu 1), The issue might be related to slurm scheduler, log comes below:

cmbuild -F --fast --symfrac 0.5  --wpb --p7ere 0.38  --EmN 200 --EvN 200 --ElfN 200 --EgfN 200 --enone '/export/galaxy-central/database/files/000/dataset_144.dat' '/export/galaxy-central/database/files/000/dataset_106.dat'   && cmcalibrate -L 1.6 --gtailn 250 --ltailn 750 --seed 181 --beta 1e-15    --cpu "${GALAXY_SLOTS:-2}" '/export/galaxy-central/database/files/000/dataset_144.dat']
galaxy.jobs.runners DEBUG 2017-11-21 14:19:04,306 (50) command is: rm -rf working; mkdir -p working; cd working; /export/galaxy-central/database/job_working_directory/000/50/tool_script.sh; return_code=$?; cd '/export/galaxy-central/database/job_working_directory/000/50'; 
[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True
python "/export/galaxy-central/database/job_working_directory/000/50/set_metadata_g9oJJe.py" "/export/galaxy-central/database/job_working_directory/000/50/registry.xml" "/export/galaxy-central/database/job_working_directory/000/50/working/galaxy.json" "/export/galaxy-central/database/job_working_directory/000/50/metadata_in_HistoryDatasetAssociation_144_z9rjR5,/export/galaxy-central/database/job_working_directory/000/50/metadata_kwds_HistoryDatasetAssociation_144_DptCYc,/export/galaxy-central/database/job_working_directory/000/50/metadata_out_HistoryDatasetAssociation_144_9gjdSY,/export/galaxy-central/database/job_working_directory/000/50/metadata_results_HistoryDatasetAssociation_144_Jichyc,/export/galaxy-central/database/files/000/dataset_144.dat,/export/galaxy-central/database/job_working_directory/000/50/metadata_override_HistoryDatasetAssociation_144_asnY13" 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.drmaa DEBUG 2017-11-21 14:19:04,388 (50) submitting file /export/galaxy-central/database/job_working_directory/000/50/galaxy_50.sh
galaxy.jobs.runners.drmaa DEBUG 2017-11-21 14:19:04,388 (50) native specification is: --ntasks=1 --share
galaxy.jobs.runners.drmaa INFO 2017-11-21 14:19:04,392 (50) queued as 51
galaxy.jobs DEBUG 2017-11-21 14:19:04,392 (50) Persisting job destination (destination id: slurm_cluster)

==> /home/galaxy/logs/slurmctld.log <==
[2017-11-21T14:19:04.391] _slurm_rpc_submit_batch_job JobId=51 usec=1189
[2017-11-21T14:19:04.395] sched: Allocate JobId=51 NodeList=c9a44253b50b #CPUs=1

==> /home/galaxy/logs/slurmd.log <==
[2017-11-21T14:19:04.413] Launching batch job 51 for UID 1450

==> /home/galaxy/logs/handler1.log <==
galaxy.jobs.runners.drmaa DEBUG 2017-11-21 14:19:04,848 (50/51) state change: job is running

Galaxy tour

• a simple Galaxy UI tool
• A Galaxy tour that guides through an entire clustering step.
• Link both from the front page