On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page and on the teaching cluster at the [[Software on Teaching Cluster]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]] or [[Software on Teaching Cluster]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

The '''file transfer''' nodes ('''xfer''' nodes) do not have environment modules installed. File transfer utilities are installed centrally on the xfer nodes and available on the users' default PATH. Such utilities include bs (basespace-cli), fpsync, rclone, rsync, etc.
https://wiki.gacrc.uga.edu/wiki/Main_Page

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 1300 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-













| [[AlphaFold-Sapelo2|AlphaFold]] || 2.2.4, 2.3.1, 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[AMBER-Sapelo2|AMBER]] || 22 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
















| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|| [[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.2, 2.6.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[BionanoSolve-Sapelo2|BionanoSolve]] || 3.6.1-11162020 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[BioPython-Sapelo2|BioPython]] || 1.79 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[Biopython-Teaching|Biopython]] || 1.79 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




| [[BLAST+-Sapelo2|BLAST+]] || 2.12.0, 2.13.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] ||[[File:Up20.png|20px|link=#top]]
|- -->
| [[BLAST+-Teaching|BLAST+]] || 2.12.0, 2.13.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[BLAST-Teaching|BLAST]] || 2.2.26 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Bowtie2-Teaching|Bowtie2]] || 2.4.1, 2.4.4, 2.4.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[BUSCO-Sapelo2|BUSCO]] || 4.0.5, 4.0.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




| [[Cactus-Sapelo2|Cactus]] || 2.6.7, 2.7.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

| [[Canu-Sapelo2|Canu]] || 2.2||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 1.2.0, 2.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[Chimera-Teaching|Chimera]] || 1.16 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-























| [[cryoSPARC-Sapelo2|CryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Cromwell-Sapelo2|Cromwell]] || 56 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|[[CUDA-Sapelo2|CUDA]] || 11.3.1, 11.4.1, 11.7.0, 12.0.0 ||[[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Cytoscape-Teaching|Cytoscape]] || 3.9.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Flankophile-Sapelo2|Flankophile]] || 0.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




















































| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[GEM-Sapelo2|GEM]] || 1.5.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[GeneMarkES-Sapelo2|GeneMarkES]] || 4.57, 4.71 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


































| [[GROMACS-Sapelo2 |GROMACS]] || 2021.5, 2023.1 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



















| [[HISAT2-Teaching|HISAT2]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.63-95.0 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




| [[IQ-Tree-Teaching|IQ-Tree]] || 1.6.12|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_241, 11.0.16, 13.0.2, 15.0.1, 17.0.6 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 5.0.0, 6.4.12 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 23Jun2022 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.25 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.04 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2023a || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Meraculous-Sapelo2|Meraculous]] || 2.2.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[MetaPhlAn4-Sapelo2|MetaPhlAn4]] || 4.0.3.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
























| [[MOTECC_qmdcp-Teaching|MOTECC_qmdcp]] || 90 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Mothur-Sapelo2|Mothur]] || 1.39.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[MrBayes-Sapelo2|MrBayes]] || 3.2.6, 3.2.7a || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


















































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 4.4.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.4 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-




|[[ORP-Sapelo2|ORP]] || 2.2.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.5.4 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[OrthoMCL-Sapelo2|OrthoMCL]] || 2.0.9 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[PAML-Teaching|PAML]] || 4.9j || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->























| [[Perl-Teaching|Perl]] || 5.34.1 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.19.2-4158 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Pong-Sapelo2|Pong]] || 1.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.18, 3.7.4, 3.8.6, 3.9.6, 3.10.4 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 2.7.18, 3.7.4, 3.8.6, 3.9.6, 3.10.4|| [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2019.10, 2020.2, 2020.6, 2020.11 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 4.1.2, 4.2.1, 4.3.1 ||[[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.1.2, 4.2.1, 4.3.1 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.4.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[RAxML-Sapelo2 |RAxML]] || 8.2.11, 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2022.46.334 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[Rstudio-Sapelo2|Rstudio]] || 2023.06.1-524 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.6, 1.14, 1.16.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[SequenceTubeMap-Sapelo2|sequenceTubeMap]] || 20230906 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






























| [[smoke-Sapelo2|smoke]] || 4.7 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

































| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 2.9.6-1,2.10.8,2.11.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.15.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[UBCG-Sapelo2|UBCG]] || 3.0
|[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

2024-02-27T15:03:49Z

Isaiah: Finished draft 1.0

[[Category:Sapelo2]]
[[Category:Software]]
[[Category:Programming]]
===Category===

Tools

===Program On===

Sapelo2

===Version===

56

===Author / Distributor===

[https://www.broadinstitute.org/ Broad Institute]

===Description===

"Cromwell is a Workflow Management System geared towards scientific workflows. Cromwell is open sourced under the [https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt BSD 3-Clause license]." [https://cromwell.readthedocs.io/en/stable/ cromwell.readthedocs.io]

=== Running Program ===
Please also refer to [[Running Jobs on Sapelo2]].
*Cromwell 56 is installed for use with Java 11.
**<code>module load cromwell/56-Java-11</code>

==== Requirements ====
To execute Cromwell as a job on Sapelo2, the following are required:

# '''Cromwell Configuration File''' (required)
## Defines how each step in the workflow should be initialized.
# '''WDL File''' (required)
## Defines the workflow itself.
# '''Inputs File''' (optional but recommended)
## Defines the inputs to the workflow.
# '''Options File''' (optional)
## Defines any additional options.
# '''Job Submission Script''' (required)

==== Example Requirements ====

====='''Example Configuration File'''=====
Cromwell requires a configuration file that includes instructions for how to execute workflows.

The maintainers of Cromwell provide short and intuitive documentation and tutorials to help understand and write a Cromwell configuration file:

* https://cromwell.readthedocs.io/en/stable/tutorials/ConfigurationFiles/
* https://cromwell.readthedocs.io/en/stable/backends/SLURM/
* https://cromwell.readthedocs.io/en/stable/tutorials/HPCIntro/

Reviewing the content at the links above can help to understand the following Cromwell configuration file that has been adapted for Sapelo2 (based on [https://github.com/broadinstitute/cromwell/blob/e914bec7fe65350de1389191d051b845462c1f81/cromwell.example.backends/slurm.conf their SLURM example]).

The following file can also be found at <code>/usr/local/training/Cromwell/cromwell-gacrc.conf</code>:

======<code>cromwell-gacrc.conf</code>======
<syntaxhighlight lang="java">
backend {
default = slurm

providers {
slurm {
actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
config {
runtime-attributes = """
String partition = "batch"
Int ntasks = 1
Int cpus_per_task = 8
Int memory = 8000
Int time = 10
"""
submit = """
sbatch \
--job-name=${job_name} \
--partition=${partition} \
--ntasks=${ntasks} \
--cpus-per-task=${cpus_per_task} \
--mem=${memory} \
--time=${time} \
--output=${out} \
--error=${err} \
--chdir=${cwd} \
--wrap "/usr/bin/env bash ${script}"
"""
kill = "scancel ${job_id}"
check-alive = "squeue -j ${job_id}"
job-id-regex = "Submitted batch job (\\d+).*"
}
}
}
}
</syntaxhighlight>

===== '''Example WDL (Workflow Description Language) File''' =====
Cromwell executes workflows written in ''WDL'' ([https://cromwell.readthedocs.io/en/stable/LanguageSupport/ Cromwell Language Support]). The Cromwell maintainers provide an [https://cromwell.readthedocs.io/en/stable/tutorials/FiveMinuteIntro/ example ''WDL''] in their documentation.

The following workflow incorporates the same ''Bowtie2'' example covered in the [[Training#Sapelo2 Cluster New User Training|Sapelo2 training workshop]], and can be found at <code>/usr/local/training/Cromwell/cromwell-bowtie2.wdl</code>:

======<code>cromwell-bowtie2.wdl</code>======
<syntaxhighlight>
workflow CromwellBowtie2 {
File input_fq
File index_dir
String index_name
Int cpus_per_task

call Bowtie2 {
input:
input_fq = input_fq,
index_dir = index_dir,
index_name = index_name,
cpus_per_task = cpus_per_task,
}
}

task Bowtie2 {
File input_fq
File index_dir
String index_name
Int cpus_per_task

command {
bowtie2 -p ${cpus_per_task} -x ${index_dir}/${index_name} -U ${input_fq} > alignments.output
}
output {
File out = "alignments.output"
}
}
</syntaxhighlight>
A WDL file contains a task-by-task description of a workflow. The first block is the ''<code>workflow</code>'' block, wherein tasks are called. Each task is described in its own ''<code>task</code>'' block. To an extent, it can be helpful to consider the ''<code>workflow</code>'' block as analogous to the ''<code>main</code>'' function, and the ''<code>task</code>'' blocks as analogous to ''<code>functions</code>''.

For more thorough information about WDL, refer to their [https://github.com/openwdl/wdl/blob/main/versions/development/SPEC.md language specification documentation]. More WDL examples can be found [https://github.com/openwdl/learn-wdl/ here].

While the paths to input data can be written in the WDL file directly, it is considered best practice to supply them at runtime instead for re-usability. This is a convenient feature when importing WDL files from other groups, as it removes the need to edit hardcoded values.

===== '''Example Workflow Input File''' =====
In Cromwell, ''Workflow Input Files'' are written in JSON. They are specified with the <code>''--inputs''</code> flag when Cromwell is executed at the [https://cromwell.readthedocs.io/en/stable/CommandLine/#run command line]. These files define the requirements of the workflow, such as input files, or other input values. Specifying these input values in a separate file prevents the need to hardcode inputs in the original workflow file.

Continuing with the above Example WDL File, the <code>CromwellBowtie2</code> workflow utilizes the following values:<syntaxhighlight>
File input_fq
File index_dir
String index_name
Int threads
</syntaxhighlight>The following JSON file provides definitions for each of these values, and can be found at <code>/usr/local/training/Cromwell/inputs.json</code>:

======<code>inputs.json</code>======
<syntaxhighlight lang="json">
{ "CromwellBowtie2.input_fq": "myreads.fq",
"CromwellBowtie2.index_dir": "index",
"CromwellBowtie2.index_name": "lambda_virus",
"CromwellBowtie2.cpus_per_task": "8"
}
</syntaxhighlight><code>--inputs input.json</code>

The example data referenced in this JSON file can be found at the following locations:

* <code>/usr/local/training/Cromwell/index</code>
* <code>/usr/local/training/Cromwell/myreads.fq</code>

===== '''Example Workflow Options File''' =====
In Cromwell, ''Workflow Options Files'', are also written in JSON. They are specified with the ''<code>--options</code>'' flag when Cromwell is executed at the [https://cromwell.readthedocs.io/en/stable/CommandLine/#run command line]. These files describe the options to use during the execution of a workflow.

By default, the output of a workflow step is stored in that step's execution directory.

The following JSON file makes use of Cromwell's [https://cromwell.readthedocs.io/en/stable/wf_options/Overview/#output-copying Output Copying] capabilities to copy the output into a directory named output, and can be found at <code>/usr/local/training/Cromwell/options.json</code>:

======<code>options.json</code>======
<syntaxhighlight lang="json">
{ "final_workflow_outputs_dir": "output",
"use_relative_output_paths": true
}
</syntaxhighlight><code>--options options.json</code>

Without specifying an alternative output directory, the output would be in a location similar to the following:

<code>./cromwell-executions/CromwellBowtie2/04d44744-2a84-4b2f-bea6-492985543ace/call-Bowtie2/execution/</code>

Where <code>cromwell-executions</code> is a subdirectory of the working directory, the <code>04d44744-2a84-4b2f-bea6-492985543ace</code> directory is named at runtime, and <code>execution</code> was the working directory of the task, ''<code>Bowtie2</code>''.

'''Example Job submission Script'''

The following is an example job submission script that utilizes the files described above, and can be found at <code>/usr/local/training/Cromwell/cromwell-sub.sh</code>:<syntaxhighlight lang="bash">
#!/bin/bash
#SBATCH --job-name=cromwell-bowtie2
#SBATCH --partition=batch
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=8gb
#SBATCH --time=00:10:00
#SBATCH --output=%x.%j.out
#SBATCH --error=%x.%j.err

module load cromwell/56-Java-11
module load Bowtie2/2.4.5-GCC-11.3.0

cd $SLURM_SUBMIT_DIR

java \
-Xmx8g \
-Dconfig.file=cromwell-gacrc.conf \
-jar $EBROOTCROMWELL/cromwell.jar \
run cromwell-bowtie2.wdl \
--inputs inputs.json \
--options options.json
</syntaxhighlight>Where:

* <code>-Xmx8g</code> instructs the Java Virtual Machine to allocate 8g of memory, which is equal to the amount requested in the SLURM header (<code>--mem=8gb</code>).
* <code>-Dconfig.file=cromwell-gacrc.conf</code> is the path to the configuration file.
* <code>-jar $EBROOTCROMWELL/cromwell.jar</code> is the Java Archive to run, which in this case is the Cromwell executable.
* <code>run cromwell-bowtie2.wdl</code> contains the subcommand, <code>run</code>, and instructs Cromwell to run the workflow in [https://cromwell.readthedocs.io/en/stable/CommandLine/#run Command Line] mode.
* <code>--inputs inputs.json</code> specifies the workflow inputs are defined in the <code>inputs.json</code> file.
* <code>--options options.json</code> specifies any additional workflow options are defined in the <code>options.json</code> file.

==== Running the example ====
To run the above example, navigate to scratch and copy the files into the working directory:<syntaxhighlight lang="bash">
cd /scratch/$USER
cp -r /usr/local/training/Cromwell/* ./
</syntaxhighlight>Once copied, the job can be submitted with <code>sbatch</code>:<syntaxhighlight lang="bash">
sbatch cromwell-sub.sh
</syntaxhighlight>

=== Installation ===

* Version 56: Installed using EasyBuild.

=== System ===

* 64-bit Linux

Cromwell-Sapelo2

2024-02-26T22:07:29Z

Isaiah: Added example WDL, inputs.json, and options.json sections and files

Cromwell-Sapelo2

2024-02-26T20:55:58Z

Isaiah: Added example config file

2023-09-05T17:45:42Z

Isaiah: Isaiah moved page SequenceTubeMap to SequenceTubeMap-Sapelo2: Fix name

=== Category ===
Bioinformatics

=== Program On ===
[https://github.com/vgteam/sequenceTubeMap GitHub]

=== Version ===
N/A

=== Author / Distributor ===
'''[https://vgteam.github.io/ vgteam]'''

=== Description ===
''"A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg."''

=== Running Program ===

==== Initial Setup ====
Before a user can run this program, it first needs to be setup in a directory of the user's choosing such as the home or scratch directory.

===== Enter Interactive Job =====
This program should be run from within an '''interactive job''', which can be started by issuing the following from a login node:<syntaxhighlight lang="bash">
interact
</syntaxhighlight>

===== Load Dependent Modules =====
As of September 5th, 2023, the dependencies for this program are '''NodeJS''', '''NPM''', and '''vg'''. The '''NPM''' program is included in our '''NodeJS''' module, so the only modules necessary are '''NodeJS''' and '''vg''', which can be loaded with the following:

'''NodeJS'''<syntaxhighlight lang="bash">
module load nodejs/18.12.1-GCCcore-11.3.0
</syntaxhighlight>'''vg'''<syntaxhighlight lang="bash">
module load vg/1.50.1
</syntaxhighlight>

===== Clone Repository =====
From within the directory that will serve to contain this project, clone the '''sequenceTubeMap''' repository:<syntaxhighlight lang="bash">
git clone https://github.com/vgteam/sequenceTubeMap.git
</syntaxhighlight>

===== Install NPM dependencies =====
This program depends on a few other programs from '''NPM'''. To install them, first enter into the '''sequenceTubeMap''' directory that was created when the repository was cloned in the previous step:<syntaxhighlight lang="bash">
cd sequenceTubeMap
</syntaxhighlight>Then, use '''NPM''' to install the additional programs into the project's directory:<syntaxhighlight lang="bash">
npm install
</syntaxhighlight>

===== Build the Frontend =====
Once the additional dependencies have been installed with '''NPM''', '''sequenceTubeMap''' will need to be built:<syntaxhighlight lang="bash">
npm run build
</syntaxhighlight>

==== Starting the server ====
As long as the previous steps have been completed, the program can be started and used when needed. Starting the program is as simple as navigating to the directory in which it is located, and running the server.

===== Enter Interactive Job =====
Unless already in an interactive job, it is necessary to enter into one before loading the modules and starting the server:<syntaxhighlight lang="bash">
interact
</syntaxhighlight>

===== Load Dependent Modules =====
The same versions of the modules that were loaded when performing the initial setup for '''sequenceTubeMap''' should be loaded whenever attempting to run the software:

'''NodeJS'''<syntaxhighlight lang="bash">
module load nodejs/18.12.1-GCCcore-11.3.0
</syntaxhighlight>'''vg'''<syntaxhighlight lang="bash">
module load vg/1.50.1
</syntaxhighlight>

===== Navigate to sequenceTubeMap =====
Unless already in the '''sequenceTubeMap''' directory, change to the location of that directory:<syntaxhighlight lang="bash">
cd /path/to/sequenceTubeMap
</syntaxhighlight>

===== Obtain IP Address =====
Obtain the IP address of the server that will host '''sequenceTubeMap''' for use in the next step:<syntaxhighlight lang="bash">
hostname -i
</syntaxhighlight>

===== Configure SSH Tunnel =====
It will be necessary to use SSH tunneling to connect to the web frontend from within a web browser. Please note that '''this step is to be performed on your local computer'''. It is recommended to setup the SSH tunnel from a new, separate terminal. Currently, the program is hard-coded to run on port 3000, but this can be changed by editing a few files as demonstrated later on this page.

====== SSH Tunneling from Mac or Linux ======
From your local terminal, issue the following command while making sure to replace '''HOST''' with the actual IP address obtained in the previous step and '''MyID''' with your actual MyID:<syntaxhighlight lang="bash">
ssh -N -L 3000:HOST:3000 MyID@sapelo2.gacrc.uga.edu
</syntaxhighlight>

====== SSH Tunneling from Windows ======
Download the '''[https://the.earth.li/~sgtatham/putty/latest/x86/plink.exe plink program]''', open a command window--the current directory of this command window should contain the ''plink.exe'' file--and execute the following command, replacing '''HOST''' with the actual IP address obtained in the previous step and '''MyID''' with your actual MyID:<syntaxhighlight lang="powershell">
plink -ssh -N -L 3000:HOST:3000 MyID@sapelo2.gacrc.uga.edu
</syntaxhighlight>

===== Launch the Program =====
To start the program, return to the terminal in which the interactive session is running, and execute the following command from within the '''sequenceTubeMap''' directory:<syntaxhighlight lang="bash">
npm run serve
</syntaxhighlight>

==== Connecting to the Server ====
To connect to the server, simply open a web browser on the computer connected to the SSH tunnel, and navigate to http://localhost:3000 in the URL bar.

=== Running Program on Different Port ===
As of September 5th, 2023 '''sequenceTubeMap''' is hard-coded to run on port 3000. As a result, using an alternative port number will require manually changing a few files.

The following commands, if issued from within the '''sequenceTubeMap''' directory, will change the necessary files to use port 8942 instead:<syntaxhighlight lang="bash">
sed -i "s/3000/8942/g" server.mjs
sed -i "s/3000/8942/g" setupProxy.js
sed -i "s/3000/8942/g" util/demo-data.js
</syntaxhighlight>If a port is used other than port 3000, use the same number when setting up SSH tunneling:<syntaxhighlight lang="bash">
ssh -N -L 8942:HOST:8942 MyID@sapelo2.gacrc.uga.edu
</syntaxhighlight>Make sure to connect to the correct corresponding port number, http://localhost:8942, when connecting from a web browser as well.

=== Documentation ===
Please reference the program's GitHub page at https://github.com/vgteam/sequenceTubeMap for further reading.

=== System ===
64-bit Linux