Snakemake run test for SO question https://stackoverflow.com/q/78260730/8508004

Snakemake run test for SO question 78260730.ipynb

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   "cell_type": "markdown",
   "id": "9ca6ae4a-2fbc-449a-ba5e-e5193220baff",
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   "source": [
    "## Snakemake run test for SO https://stackoverflow.com/q/78260730/8508004\n",
    "\n",
    "Ran in session launched from [here](https://github.com/fomightez/pdbepisa-binder) via clicking 'launch binder' badge. (Or click badge below for a fresh session!)\n",
    "\n",
    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/fomightez/pdbepisa-binder/main?urlpath=%2Fnotebooks%2Findex.ipynb)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "bafc96b3-29d8-44fd-8a58-5866542a4ce0",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " apt.txt       README.md\n",
      " index.ipynb   requirements.txt\n",
      " LICENSE      'Snakemake run test for SO question 78260730.ipynb'\n",
      " \u001b[0m\u001b[01;34mnotebooks\u001b[0m/\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "c389f424-d490-4092-afed-2d36ec658e18",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Writing 's' (str) to file 'Snakefile'.\n"
     ]
    }
   ],
   "source": [
    "s='''rule A:\n",
    "        input:\n",
    "                i = 'B1477.all_merged_3split_dedupped_sorted.bam'\n",
    "        output:\n",
    "                o = 'B1477.all_merged_3split_dedupped_sorted2.bam'\n",
    "        shell:\n",
    "                \"cat {input.i} > {output.o}\"\n",
    "'''\n",
    "%store s >Snakefile"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3be94589-cefa-46b5-8902-8e4b4ddf7b79",
   "metadata": {},
   "source": [
    "Started runnng with only a `Snakefile` that had the above content."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "411ce30a-4a16-4506-b579-fd845dedaa50",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[33mBuilding DAG of jobs...\u001b[0m\n",
      "\u001b[31mMissingInputException in line 1 of /home/jovyan/Snakefile:\n",
      "Missing input files for rule A:\n",
      "    output: B1477.all_merged_3split_dedupped_sorted2.bam\n",
      "    affected files:\n",
      "        B1477.all_merged_3split_dedupped_sorted.bam\u001b[0m\n"
     ]
    }
   ],
   "source": [
    "!snakemake --cores 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "68736e64-1d0e-43c0-926a-3680de406a9f",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " apt.txt       README.md\n",
      " index.ipynb   requirements.txt\n",
      " LICENSE       Snakefile\n",
      " \u001b[0m\u001b[01;34mnotebooks\u001b[0m/   'Snakemake run test for SO question 78260730.ipynb'\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "edb2993f-2c95-4bcb-ad66-c737d6e6c54f",
   "metadata": {},
   "source": [
    "Make the input file."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "1e551dfa-4008-4bd1-a010-c1a7f83b3d9f",
   "metadata": {},
   "outputs": [],
   "source": [
    "!touch B1477.all_merged_3split_dedupped_sorted.bam"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dc6f344b-4598-4c04-b27f-42f7e0850b03",
   "metadata": {},
   "source": [
    "Now try again."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "a7cd6cb9-80d8-405f-b77b-d21f6928477c",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[33mBuilding DAG of jobs...\u001b[0m\n",
      "\u001b[33mUsing shell: /bin/bash\u001b[0m\n",
      "\u001b[33mProvided cores: 1 (use --cores to define parallelism)\u001b[0m\n",
      "\u001b[33mRules claiming more threads will be scaled down.\u001b[0m\n",
      "\u001b[33mJob stats:\n",
      "job      count    min threads    max threads\n",
      "-----  -------  -------------  -------------\n",
      "A            1              1              1\n",
      "total        1              1              1\n",
      "\u001b[0m\n",
      "\u001b[33mSelect jobs to execute...\u001b[0m\n",
      "\u001b[32m\u001b[0m\n",
      "\u001b[32m[Tue Apr  2 17:52:26 2024]\u001b[0m\n",
      "\u001b[32mrule A:\n",
      "    input: B1477.all_merged_3split_dedupped_sorted.bam\n",
      "    output: B1477.all_merged_3split_dedupped_sorted2.bam\n",
      "    jobid: 0\n",
      "    resources: tmpdir=/tmp\u001b[0m\n",
      "\u001b[32m\u001b[0m\n",
      "\u001b[32m[Tue Apr  2 17:52:26 2024]\u001b[0m\n",
      "\u001b[32mFinished job 0.\u001b[0m\n",
      "\u001b[32m1 of 1 steps (100%) done\u001b[0m\n",
      "\u001b[33mComplete log: .snakemake/log/2024-04-02T175226.183902.snakemake.log\u001b[0m\n"
     ]
    }
   ],
   "source": [
    "!snakemake --cores 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "92f2c41e-0634-4dc0-834d-0dd9774c47b1",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " apt.txt\n",
      " B1477.all_merged_3split_dedupped_sorted2.bam\n",
      " B1477.all_merged_3split_dedupped_sorted.bam\n",
      " index.ipynb\n",
      " LICENSE\n",
      " \u001b[0m\u001b[01;34mnotebooks\u001b[0m/\n",
      " README.md\n",
      " requirements.txt\n",
      " Snakefile\n",
      "'Snakemake run test for SO question 78260730.ipynb'\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1c98de98-a163-4982-a413-6e74c70b742a",
   "metadata": {},
   "source": [
    "Worked!"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6bb0d2c8-9729-4da2-a54f-1e3004702f6b",
   "metadata": {},
   "source": [
    "#### What if remove the output and do dry run?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "10be6a4d-c233-46c7-8ab2-2dff15534071",
   "metadata": {},
   "outputs": [],
   "source": [
    "!rm -rf B1477.all_merged_3split_dedupped_sorted2.bam"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "73d5dbb3-f4f4-4901-82b5-ed505f89b7a0",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " apt.txt\n",
      " B1477.all_merged_3split_dedupped_sorted.bam\n",
      " index.ipynb\n",
      " LICENSE\n",
      " \u001b[0m\u001b[01;34mnotebooks\u001b[0m/\n",
      " README.md\n",
      " requirements.txt\n",
      " Snakefile\n",
      "'Snakemake run test for SO question 78260730.ipynb'\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "80c41494-f8b7-425d-ada4-a3ea539e1c04",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[33mBuilding DAG of jobs...\u001b[0m\n",
      "\u001b[33mJob stats:\n",
      "job      count    min threads    max threads\n",
      "-----  -------  -------------  -------------\n",
      "A            1              1              1\n",
      "total        1              1              1\n",
      "\u001b[0m\n",
      "\u001b[32m\u001b[0m\n",
      "\u001b[32m[Tue Apr  2 17:52:32 2024]\u001b[0m\n",
      "\u001b[32mrule A:\n",
      "    input: B1477.all_merged_3split_dedupped_sorted.bam\n",
      "    output: B1477.all_merged_3split_dedupped_sorted2.bam\n",
      "    jobid: 0\n",
      "    resources: tmpdir=/tmp\u001b[0m\n",
      "\u001b[32m\u001b[0m\n",
      "\u001b[33mJob stats:\n",
      "job      count    min threads    max threads\n",
      "-----  -------  -------------  -------------\n",
      "A            1              1              1\n",
      "total        1              1              1\n",
      "\u001b[0m\n",
      "\u001b[33mThis was a dry-run (flag -n). The order of jobs does not reflect the order of execution.\u001b[0m\n"
     ]
    }
   ],
   "source": [
    "!snakemake -n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6d6c7086-ccfa-49ad-8713-4fcc8074d7e2",
   "metadata": {},
   "source": [
    "Still seems to work without error."
   ]
  }
 ],
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