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Commit 6521d82c authored by Fortune Iriaye's avatar Fortune Iriaye
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Merge branch 'master' into 'master'

Converted this repo for use with FSL

See merge request rc/bc-uab-fsl!1
parents 9489da4f b38ce3a4
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......@@ -41,10 +41,10 @@ attributes:
version:
widget: select
label: "IGV version"
help: "This defines the version of IGV you want to load."
label: "FSL version"
help: "This defines the version of FSL you want to load."
options:
- [ "2.12.2-Java-11", "IGV/2.12.2-Java-11" ]
- [ "6.0.3", "FSL/6.0.3" ]
form:
- version
......
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---
name: IGV
name: FSL - FMRIB Software Library
category: Interactive Apps
subcategory: GUIs
role: batch_connect
description: |
This app will launch a [Integrative Genomics Viewer(IGV)] on the [Cheaha]. You will be able
to interact with the IGV through a VNC session.
This app will launch a [FMRIB Software Library (FSL)] on [Cheaha]. You will be able
to interact with FSL through a VNC session.
[Integrative Genomics Viewer(IGV)]: https://software.broadinstitute.org/software/igv/
[Cheaha]: https://docs.uabgrid.uab.edu
[FMRIB Software Library (FSL)]: https://fsl.fmrib.ox.ac.uk/fsl/docs/#/
[Cheaha]: https://rc.uab.edu
......@@ -25,13 +25,13 @@ cd "${HOME}"
) &
#
# Start Integrative Genomics Viewer
# Start FMRIB Software Library
#
# Load the required environment
module load <%= context.version %>
# Launch IGV
module load FSL/6.0.3
# Launch FSL
module list
set -x
igvtools_gui.command &
igv.sh
source /share/apps/rc/software/FSL/6.0.3/fsl/etc/fslconf/fsl.sh
fsl
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