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Update hugen.md
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fangpingmu authored Dec 30, 2024
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15 changes: 8 additions & 7 deletions docs/web-portals/hugen.md
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Expand Up @@ -203,13 +203,13 @@ R CMD BATCH test.R test.txt

<p>When you start Jupyter Notebook/Lab, the working directory is the home directory. You can use softlink trick to navigate to course storage.</p>

<p>Logon ondemand.htc.crc.pitt.edu, click Clusters -&gt; &gt;_HTC Shell Access</p>
<p>Logon hugen.crc.pitt.edu, click Clusters -&gt; &gt;_teach Shell Access</p>

<pre>
[fmu@login0b ~]$ mkdir -p /ix/genomics/demo/users/fmu # create a folder
[fmu@login0b ~]$ chmod 700 /ix/genomics/demo/users/fmu # change the permission
[fmu@login0b ~]$ ln -s /ix/genomics/demo/users/fmu my_course_data # generate a softlink to home directory
[fmu@login0b ~]$</pre>
[fmu@login3 ~]$ mkdir -p /ix1/hugen2071-2024f/users/fmu # create a folder
[fmu@login3 ~]$ chmod 700 /ix1/hugen2071-2024f/users/fmu # change the permission
[fmu@login3 ~]$ ln -s /ix1/hugen2071-2024f/users/fmu my_course_data # generate a softlink to home directory
[fmu@login3 ~]$</pre>

<p>Each student can navigate to his/her own my_course_data from Jupyter Lab.</p>

Expand All @@ -218,14 +218,15 @@ R CMD BATCH test.R test.txt
<pre>
#!/bin/bash
#SBATCH --job-name ExampleJob
#SBATCH --account=course-2023s # use your course allocation
#SBATCH -M teach # use teach cluster
#SBATCH --account=hugen2071-2024f # use your course allocation
#SBATCH --nodes=1 # request a single node
#SBATCH -c 1 # request 1 core
#SBATCH --time=01:00:00 # 1 hour walltime

# use the custom conda environment
module load python/ondemand-jupyter-python3.10
source activate /ix/genomics/demo/software/env
source activate /ix1/hugen2071-2024f/software/env

# You can also use other modules
# module load hisat2/2.2.1
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