Merge pull request #3 from Harvard-ATG/heb115

Add customizations for use in HEB 115

local/heb115.yml.erb

@@ -0,0 +1,84 @@
+# Batch Connect app configuration file
+#
+# @note Used to define the submitted cluster, title, description, and
+#   hard-coded/user-defined attributes that make up this Batch Connect app.
+<%-
+# User POSIX groups are checked against a list of Canvas Course IDs, which are 
+# expected to be present in group names following the convention 
+# `canvas<canvas_id>-<group_id>`. To add to this list, add a Canvas Course ID 
+# and comment it with the title of the course.
+userGroups = OodSupport::User.new.groups.sort_by(&:id).map(&:name).flat_map{ |str| str.scan(/^canvas(\d+)-\d+/) }.flatten
+enabledGroups = [
+  "135510", # HUIT Open OnDemand Testing
+  "139860"  # HEB 115: Investigating the Human Genome
+]
+
+def arrays_have_common_element(array1, array2)
+  # Use the `&` operator to get the intersection of the two arrays
+  # If the intersection is not empty, return true, otherwise false
+  !(array1 & array2).empty?
+end
+
+# Check if the groups that the user is in match any of the courses that should 
+# have access to this app.
+
+if arrays_have_common_element(userGroups, enabledGroups)
+  cluster="*"
+else
+  cluster="disable_this_app"
+end
+-%>
+---
+
+# Set cluster from group. "*" runs on whatever cluster is available, and 
+# "disable_this_app" hides the app from view.
+cluster: "<%= cluster %>"
+
+title: "Jupyter Lab - HEB 115"
+
+# Define attribute values that aren't meant to be modified by the user within
+# the Dashboard form
+attributes:
+  # Set the corresponding modules that need to be loaded for Jupyter to run
+  #
+  # @note It is called within the batch job as `module load <modules>` if
+  #   defined
+  # @example Do not load any modules
+  #     modules: ""
+  # @example Using default python module
+  #     modules: "python"
+  # @example Using specific python module
+  #     modules: "python/3.5"
+  # @example Using combination of modules
+  #     modules: "python/3.5 cuda/8.0.44"
+  environment: heb115
+
+  spack: "/shared/spack"
+
+  custom_num_cores:
+    widget: "number_field"
+    label: "Number of CPUs"
+    value: 1
+    min: 1
+    max: 4
+    step: 1
+
+  # Any extra command line arguments to feed to the `jupyter notebook ...`
+  # command that launches the Jupyter notebook within the batch job
+  extra_jupyter_args: ""
+
+# All of the attributes that make up the Dashboard form (in respective order),
+# and made available to the submit configuration file and the template ERB
+# files
+#
+# @note You typically do not need to modify this unless you want to add a new
+#   configurable value
+# @note If an attribute listed below is hard-coded above in the `attributes`
+#   option, then it will not appear in the form page that the user sees in the
+#   Dashboard
+form:
+  - environment
+  - spack
+  - extra_jupyter_args
+  - bc_num_hours
+  - custom_num_cores

manifest.yml

@@ -1,7 +1,12 @@
 ---
-name: Jupyter Notebook (spack)
+name: Jupyter Lab
 category: Interactive Apps
 subcategory: Servers
 role: batch_connect
 description: |
-  This app will launch a Jupyter Notebook server on one or more nodes. This configuration uses spack to load Jupyter Lab.
+  This app will launch a Jupyter Lab server. This configuration uses
+  [Spack](https://spack.io/) to load Jupyter Lab. The app launches outside of a
+  container, so it has access to slurm commands, but since the app is running as
+  a slurm job, the `srun` command will use the resources of the current job,
+  rather than starting a new job. That is, unless you first run an `salloc`
+  command to allocate a new interactive session first.

spack-environment/heb115/spack.yml

@@ -0,0 +1,19 @@
+# This is a Spack Environment file.
+#
+# It describes a set of packages to be installed, along with
+# configuration settings.
+spack:
+  # add package specs to the `specs` list
+  specs:
+  - admixtools
+  - bcftools
+  - plink
+  - samtools
+  - py-jupyterlab
+  - py-numpy
+  - py-pandas
+  - py-matplotlib
+  - py-scipy
+  view: true
+  concretizer:
+    unify: true