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PLINK changed to Plink #169

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55 changes: 2 additions & 53 deletions admin/submit_csg.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
"```"
]
},
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -201,7 +150,7 @@
"height": 0,
"style": "side"
},
"version": "0.22.9"
"version": "0.24.1"
}
},
"nbformat": 4,
Expand Down