From 3e13ca08a896e7d07e7835731d9d9c27b07de9ae Mon Sep 17 00:00:00 2001
From: yr542 <yr542@nyu.edu>
Date: Thu, 1 Jun 2023 15:01:15 -0400
Subject: [PATCH] PLINK changed to Plink

---
 admin/submit_csg.ipynb | 55 ++----------------------------------------
 1 file changed, 2 insertions(+), 53 deletions(-)

diff --git a/admin/submit_csg.ipynb b/admin/submit_csg.ipynb
index d590dc6..51b5398 100644
--- a/admin/submit_csg.ipynb
+++ b/admin/submit_csg.ipynb
@@ -65,12 +65,6 @@
     "sos run submit_csg.ipynb submit_csg \\\n",
     "    --cmd_file analysis_commands_20200825.txt \\\n",
     "    --dryrun\n",
-    "```\n",
-    "\n",
-    "```\n",
-    "sos run submit_csg.ipynb submit_csg2 \\\n",
-    "    --cmd_file analysis_commands_20200825.txt \\\n",
-    "    --dryrun\n",
     "```"
    ]
   },
@@ -103,52 +97,7 @@
     "    #$ -S /bin/bash\n",
     "    module load Singularity\n",
     "    module load VCFTOOLS/0.1.17\n",
-    "    module load PLINK/1.9.10 \n",
-    "    export PATH=$HOME/miniconda3/bin:$PATH\n",
-    "    set -e\n",
-    "    '''\n",
-    "    script = tpl.lstrip() + ''.join(open($[_input:r]).readlines())\n",
-    "    exe = 'cat' if $[dryrun] else 'qsub'\n",
-    "    from subprocess import Popen, PIPE\n",
-    "    import sys\n",
-    "    p = Popen(exe, shell = False, stdin = PIPE, stdout = PIPE, stderr = PIPE, close_fds = True)\n",
-    "    for item in p.communicate(script.encode(sys.getdefaultencoding())):\n",
-    "        output = item.decode(sys.getdefaultencoding()).rstrip()\n",
-    "        if output:\n",
-    "            print(output)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "kernel": "SoS"
-   },
-   "outputs": [],
-   "source": [
-    "# Job submission on CSG cluster\n",
-    "[submit_csg2]\n",
-    "# Path to job file\n",
-    "parameter: cmd_file=path\n",
-    "# Total run time allocated to the script\n",
-    "parameter: time='36:00:00'\n",
-    "# Memory allocated to a job, in terms of Gigabyte\n",
-    "parameter: mem=12\n",
-    "parameter: dryrun = False\n",
-    "input: cmd_file\n",
-    "python3: expand = '$[ ]'\n",
-    "    tpl = '''\n",
-    "    #!/bin/sh\n",
-    "    #$ -l h_rt=$[time]\n",
-    "    #$ -l h_vmem=$[mem+6]G\n",
-    "    #$ -N gatk_joint_call\n",
-    "    #$ -cwd\n",
-    "    #$ -j y\n",
-    "    #$ -q csg2.q -l t_pri\n",
-    "    #$ -S /bin/bash\n",
-    "    module load Singularity\n",
-    "    module load VCFTOOLS/0.1.17\n",
-    "    module load PLINK/1.9.10 \n",
+    "    module load Plink/1.9.10 \n",
     "    export PATH=$HOME/miniconda3/bin:$PATH\n",
     "    set -e\n",
     "    '''\n",
@@ -201,7 +150,7 @@
     "height": 0,
     "style": "side"
    },
-   "version": "0.22.9"
+   "version": "0.24.1"
   }
  },
  "nbformat": 4,