Add files via upload

Author: flowscience

notebooks/IPFS_uploadDownload.ipynb

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+{"nbformat":4,"nbformat_minor":0,"metadata":{"colab":{"provenance":[],"authorship_tag":"ABX9TyMH6A7fEhd449IBVATAgS/n"},"kernelspec":{"name":"python3","display_name":"Python 3"},"language_info":{"name":"python"}},"cells":[{"cell_type":"code","source":["# Store your input data on IPFS\n","\n","# Install the IPFS HTTP Client\n","!pip install ipfshttpclient\n","\n","import ipfshttpclient\n","\n","def upload_to_ipfs(file_path):\n","    try:\n","        client = ipfshttpclient.connect('/dns/ipfs.infura.io/tcp/5001/https')\n","        res = client.add(file_path)\n","        return res\n","    except Exception as e:\n","        print(f\"An error occurred: {e}\")\n","        return None\n","\n","sdf_CID = upload_to_ipfs('https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/ATP_ideal.sdf')\n","print(sdf_CID)"],"metadata":{"id":"hzLoLxEu0D6r"},"execution_count":null,"outputs":[]},{"cell_type":"code","source":["import os\n","\n","def download_and_upload_file(url, directory, filename=None):\n","    local_filename = download_file(url, directory, filename)\n","    file_path = os.path.join(directory, local_filename)\n","    res = upload_to_ipfs(file_path)\n","    return res"],"metadata":{"id":"gC4ODHBf0a3z"},"execution_count":null,"outputs":[]}]}

notebooks/labdao/Colabfold_plex_0.8.18.ipynb

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+{"nbformat":4,"nbformat_minor":0,"metadata":{"colab":{"provenance":[{"file_id":"1lXnLBSU1OipzjvuDCGAKAqCYyGUV0g-3","timestamp":1689292810500},{"file_id":"14zrnkNGyi3OGn5VG2ORboomI5AMEMHzm","timestamp":1689128534406}]},"kernelspec":{"name":"python3","display_name":"Python 3"},"language_info":{"name":"python"}},"cells":[{"cell_type":"code","execution_count":null,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"CFMpQQ8hhivp","executionInfo":{"status":"ok","timestamp":1689293087291,"user_tz":420,"elapsed":8781,"user":{"displayName":"Elijah Spina","userId":"09538733801989465977"}},"outputId":"13b34f1c-ab50-4f60-dc7a-e1aaf8b96ec6"},"outputs":[{"output_type":"stream","name":"stdout","text":["Collecting PlexLabExchange\n","  Downloading PlexLabExchange-0.8.17-py3-none-manylinux2014_x86_64.whl (26.9 MB)\n","\u001b[2K     \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m26.9/26.9 MB\u001b[0m \u001b[31m49.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n","\u001b[?25hInstalling collected packages: PlexLabExchange\n","Successfully installed PlexLabExchange-0.8.17\n","Requirement already satisfied: requests in /usr/local/lib/python3.10/dist-packages (2.27.1)\n","Requirement already satisfied: urllib3<1.27,>=1.21.1 in /usr/local/lib/python3.10/dist-packages (from requests) (1.26.16)\n","Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/dist-packages (from requests) (2023.5.7)\n","Requirement already satisfied: charset-normalizer~=2.0.0 in /usr/local/lib/python3.10/dist-packages (from requests) (2.0.12)\n","Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/dist-packages (from requests) (3.4)\n"]}],"source":["!pip install PlexLabExchange\n","!pip install requests"]},{"cell_type":"code","source":["!mkdir /fastQCdemo\n","PROJECT_DIR = \"/fastQCdemo\"\n","JOBS_DIR = f\"{PROJECT_DIR}/jobs\""],"metadata":{"id":"JyM22v59jaAl"},"execution_count":null,"outputs":[]},{"cell_type":"code","source":["import requests\n","import os\n","\n","def download_file(url, directory, filename=None):\n","    local_filename = filename if filename else url.split('/')[-1]\n","    with requests.get(url, stream=True) as r:\n","        r.raise_for_status()\n","        with open(os.path.join(directory, local_filename), 'wb') as f:\n","            for chunk in r.iter_content(chunk_size=8192):\n","                f.write(chunk)\n","    return local_filename\n","\n","url = 'https://github.com/labdao/plex/blob/main/testdata/sequencing/fastqc/testdata.fastq' # demo FASTQ file\n","fastq_filepath = download_file(url, PROJECT_DIR)\n","\n","tool_url = \"https://github.com/labdao/plex/blob/main/tools/fastqc/fastqc.json\"\n","tool_path = download_file(tool_url, PROJECT_DIR)"],"metadata":{"id":"XRX2kGfuhpBP"},"execution_count":null,"outputs":[]},{"cell_type":"code","source":["from plex import CoreTools, plex_create\n","\n","sequences = [fastq_filepath]\n","dir_path = f\"{PROJECT_DIR}\"\n","\n","initial_io_cid = plex_create(f\"{PROJECT_DIR}/fastqc.json\", dir_path)\n"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"0VIsnPFbiFXB","executionInfo":{"status":"ok","timestamp":1689293256804,"user_tz":420,"elapsed":178,"user":{"displayName":"Elijah Spina","userId":"09538733801989465977"}},"outputId":"cc57da82-edba-4b7f-b367-f8a5e87c06ea"},"execution_count":null,"outputs":[{"output_type":"stream","name":"stdout","text":["Plex version (v0.8.3) up to date.\n","Temporary directory created: /tmp/b5cc735b-efee-4034-9e31-be2f52b4ea144259442832\n","Reading tool config:  /fastQCdemo/fastqc.json\n","Creating IO entries from input directory:  /fastQCdemo\n","Initialized IO file at:  /tmp/b5cc735b-efee-4034-9e31-be2f52b4ea144259442832/io.json\n","Initial IO JSON file CID:  QmYkj8ut1RFRGaTDAA5Dhof4iGQZ1L77uEFE3rt7Npv8BZ\n"]}]},{"cell_type":"code","source":["from plex import plex_run\n","\n","completed_io_cid, completed_io_filepath = plex_run(initial_io_cid, PROJECT_DIR)"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"Kjhr6gfCi01G","executionInfo":{"status":"ok","timestamp":1689293997680,"user_tz":420,"elapsed":723683,"user":{"displayName":"Elijah Spina","userId":"09538733801989465977"}},"outputId":"897d7b1e-36d1-4437-e8fb-7f027b4c74d2"},"execution_count":null,"outputs":[{"output_type":"stream","name":"stdout","text":["Plex version (v0.8.3) up to date.\n","Created working directory:  /fastQCdemo/3734564b-505b-4f89-9d60-d0edfd4077d4\n","Initialized IO file at:  /fastQCdemo/3734564b-505b-4f89-9d60-d0edfd4077d4/io.json\n","Processing IO Entries\n","Starting to process IO entry 0 \n","Job running...\n","Bacalhau job id: 696335cf-2713-4637-9f46-a6aeb5056364 \n","Error processing IO entry 0 \n","error cleaning Bacalhau output directory: open /fastQCdemo/3734564b-505b-4f89-9d60-d0edfd4077d4/entry-0/outputs/outputs: no such file or directory\n","Finished processing, results written to /fastQCdemo/3734564b-505b-4f89-9d60-d0edfd4077d4/io.json\n","Completed IO JSON CID: QmUYgHhKBuqhTT7L3X2QSFN6hdj81cKbqNc8fGPLLHYEmo\n"]}]},{"cell_type":"code","source":[],"metadata":{"id":"xQeDPDm2L3nB"},"execution_count":null,"outputs":[]}]}

notebooks/labdao/Copy of DiffDock.ipynb

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+{"nbformat":4,"nbformat_minor":0,"metadata":{"colab":{"provenance":[{"file_id":"14zrnkNGyi3OGn5VG2ORboomI5AMEMHzm","timestamp":1689128534406}]},"kernelspec":{"name":"python3","display_name":"Python 3"},"language_info":{"name":"python"}},"cells":[{"cell_type":"code","execution_count":1,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"CFMpQQ8hhivp","executionInfo":{"status":"ok","timestamp":1689608690745,"user_tz":420,"elapsed":11270,"user":{"displayName":"Elijah Spina","userId":"09538733801989465977"}},"outputId":"9d015231-2efd-447e-f1f8-b83ce1294785"},"outputs":[{"output_type":"stream","name":"stdout","text":["Collecting PlexLabExchange\n","  Downloading PlexLabExchange-0.8.18-py3-none-manylinux2014_x86_64.whl (26.9 MB)\n","\u001b[2K     \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m26.9/26.9 MB\u001b[0m \u001b[31m41.7 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n","\u001b[?25hInstalling collected packages: PlexLabExchange\n","Successfully installed PlexLabExchange-0.8.18\n","Requirement already satisfied: requests in /usr/local/lib/python3.10/dist-packages (2.27.1)\n","Requirement already satisfied: urllib3<1.27,>=1.21.1 in /usr/local/lib/python3.10/dist-packages (from requests) (1.26.16)\n","Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/dist-packages (from requests) (2023.5.7)\n","Requirement already satisfied: charset-normalizer~=2.0.0 in /usr/local/lib/python3.10/dist-packages (from requests) (2.0.12)\n","Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/dist-packages (from requests) (3.4)\n"]}],"source":["!pip install PlexLabExchange\n","!pip install requests"]},{"cell_type":"code","source":["!mkdir /opencann\n","PROJECT_DIR = \"/opencann\"\n","JOBS_DIR = f\"{PROJECT_DIR}/jobs\""],"metadata":{"id":"JyM22v59jaAl","executionInfo":{"status":"ok","timestamp":1689608690746,"user_tz":420,"elapsed":11,"user":{"displayName":"Elijah Spina","userId":"09538733801989465977"}}},"execution_count":2,"outputs":[]},{"cell_type":"code","source":["import requests\n","import os\n","\n","def download_file(url, directory, filename=None):\n","    local_filename = filename if filename else url.split('/')[-1]\n","    with requests.get(url, stream=True) as r:\n","        r.raise_for_status()\n","        with open(os.path.join(directory, local_filename), 'wb') as f:\n","            for chunk in r.iter_content(chunk_size=8192):\n","                f.write(chunk)\n","    return local_filename\n","\n","url = 'https://rest.uniprot.org/uniprotkb/Q71UU0.fasta' # GABAAR in humans\n","\n","gabbar_fasta_filepath = download_file(url, PROJECT_DIR)\n"],"metadata":{"id":"XRX2kGfuhpBP","executionInfo":{"status":"ok","timestamp":1689608776636,"user_tz":420,"elapsed":657,"user":{"displayName":"Elijah Spina","userId":"09538733801989465977"}}},"execution_count":5,"outputs":[]},{"cell_type":"code","source":["from plex import CoreTools, plex_create\n","\n","sequences = [gabbar_fasta_filepath]\n","dir_path = f\"{PROJECT_DIR}\"\n","\n","initial_io_cid = plex_create(CoreTools.COLABFOLD_MINI.value, dir_path)\n"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"0VIsnPFbiFXB","executionInfo":{"status":"ok","timestamp":1689608803053,"user_tz":420,"elapsed":476,"user":{"displayName":"Elijah Spina","userId":"09538733801989465977"}},"outputId":"1a6cbfff-6afd-443c-9ff1-b24c14109248"},"execution_count":7,"outputs":[{"output_type":"stream","name":"stdout","text":["Plex version (v0.8.3) up to date.\n","Temporary directory created: /tmp/5c52ae65-87eb-4c03-954a-69f34bd0406d434551327\n","Reading tool config:  QmcRH74qfqDBJFku3mEDGxkAf6CSpaHTpdbe1pMkHnbcZD\n","Creating IO entries from input directory:  /opencann\n","Initialized IO file at:  /tmp/5c52ae65-87eb-4c03-954a-69f34bd0406d434551327/io.json\n","Initial IO JSON file CID:  QmNRC3EGVGcqQ3YA5h4ZNeCf8AU4odYpoifArDUxnA82bi\n"]}]},{"cell_type":"code","source":["from plex import plex_run\n","\n","completed_io_cid, completed_io_filepath = plex_run(initial_io_cid, PROJECT_DIR)"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"Kjhr6gfCi01G","executionInfo":{"status":"ok","timestamp":1689609240548,"user_tz":420,"elapsed":422587,"user":{"displayName":"Elijah Spina","userId":"09538733801989465977"}},"outputId":"8da77d92-a0c4-4899-cb6c-e398ce7ab71d"},"execution_count":9,"outputs":[{"output_type":"stream","name":"stdout","text":["Plex version (v0.8.3) up to date.\n","Created working directory:  /opencann/b45a1d29-522b-4f1f-ae5b-67fa9f48442c\n","Initialized IO file at:  /opencann/b45a1d29-522b-4f1f-ae5b-67fa9f48442c/io.json\n","Processing IO Entries\n","Starting to process IO entry 0 \n","Job running...\n","Bacalhau job id: 297c8765-6326-4a25-a7d1-23b6285b27b2 \n","\n","Computing default go-libp2p Resource Manager limits based on:\n","    - 'Swarm.ResourceMgr.MaxMemory': \"6.8 GB\"\n","    - 'Swarm.ResourceMgr.MaxFileDescriptors': 524288\n","\n","Applying any user-supplied overrides on top.\n","Run 'ipfs swarm limit all' to see the resulting limits.\n","\n","Error processing IO entry 0 \n","error downloading Bacalhau results: failed to write to '/opencann/b45a1d29-522b-4f1f-ae5b-67fa9f48442c/entry-0/outputs/raw/QmcKV8KVsoS2eBGcx2mVRc1oHyzt96vFH78EtkQRsgX5JA': context deadline exceeded\n","Finished processing, results written to /opencann/b45a1d29-522b-4f1f-ae5b-67fa9f48442c/io.json\n","Completed IO JSON CID: QmfM4riSHSbb6xM7NxJNmPnZYt3rgnxEk1Fboyxkn1RQSV\n","2023/07/17 15:48:57 failed to sufficiently increase receive buffer size (was: 208 kiB, wanted: 2048 kiB, got: 416 kiB). See https://github.com/quic-go/quic-go/wiki/UDP-Receive-Buffer-Size for details.\n"]}]},{"cell_type":"code","source":[],"metadata":{"id":"xQeDPDm2L3nB"},"execution_count":null,"outputs":[]}]}

notebooks/labdao/Copy of GABAAR_Demo.ipynb

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+{"nbformat":4,"nbformat_minor":0,"metadata":{"colab":{"provenance":[],"authorship_tag":"ABX9TyPk7RDvJkyNXh9bzmGAw3ev"},"kernelspec":{"name":"python3","display_name":"Python 3"},"language_info":{"name":"python"}},"cells":[{"cell_type":"code","execution_count":1,"metadata":{"id":"eZlCKRGwUPpV","colab":{"base_uri":"https://localhost:8080/"},"executionInfo":{"status":"ok","timestamp":1689634653974,"user_tz":420,"elapsed":9901,"user":{"displayName":"Elijah Spina","userId":"09538733801989465977"}},"outputId":"082b6e83-e930-4b6c-f453-8520c9f222e0"},"outputs":[{"output_type":"stream","name":"stdout","text":["Collecting PlexLabExchange\n","  Downloading PlexLabExchange-0.8.18-py3-none-manylinux2014_x86_64.whl (26.9 MB)\n","\u001b[2K     \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m26.9/26.9 MB\u001b[0m \u001b[31m34.5 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n","\u001b[?25hInstalling collected packages: PlexLabExchange\n","Successfully installed PlexLabExchange-0.8.18\n","Requirement already satisfied: requests in /usr/local/lib/python3.10/dist-packages (2.27.1)\n","Requirement already satisfied: urllib3<1.27,>=1.21.1 in /usr/local/lib/python3.10/dist-packages (from requests) (1.26.16)\n","Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/dist-packages (from requests) (2023.5.7)\n","Requirement already satisfied: charset-normalizer~=2.0.0 in /usr/local/lib/python3.10/dist-packages (from requests) (2.0.12)\n","Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/dist-packages (from requests) (3.4)\n"]}],"source":["!pip install PlexLabExchange\n","!pip install requests"]},{"cell_type":"code","source":["!mkdir /fastQCdemo\n","PROJECT_DIR = \"/fastQCdemo\"\n","JOBS_DIR = f\"{PROJECT_DIR}/jobs\""],"metadata":{"id":"V1Tv1WzyUaab","executionInfo":{"status":"ok","timestamp":1689634654196,"user_tz":420,"elapsed":235,"user":{"displayName":"Elijah Spina","userId":"09538733801989465977"}}},"execution_count":2,"outputs":[]},{"cell_type":"code","source":["import requests\n","import os\n","\n","def download_file(url, directory, filename=None):\n","    local_filename = filename if filename else url.split('/')[-1]\n","    with requests.get(url, stream=True) as r:\n","        r.raise_for_status()\n","        with open(os.path.join(directory, local_filename), 'wb') as f:\n","            for chunk in r.iter_content(chunk_size=8192):\n","                f.write(chunk)\n","    return local_filename\n","\n","url = 'https://raw.githubusercontent.com/labdao/plex/main/testdata/sequencing/fastqc/testdata.fastq' # demo FASTQ file\n","fastq_filepath = download_file(url, PROJECT_DIR)\n","\n","tool_url = \"https://raw.githubusercontent.com/labdao/plex/main/tools/fastqc/fastqc.json\"\n","tool_path = download_file(tool_url, PROJECT_DIR)"],"metadata":{"id":"mnK0-udDUc9W","executionInfo":{"status":"ok","timestamp":1689634730570,"user_tz":420,"elapsed":526,"user":{"displayName":"Elijah Spina","userId":"09538733801989465977"}}},"execution_count":4,"outputs":[]},{"cell_type":"code","source":["from plex import CoreTools, plex_create\n","\n","initial_io_cid = plex_create(f\"{PROJECT_DIR}/fastqc.json\", f\"{PROJECT_DIR}\")\n","#initial_io_cid = plex_create(CoreTools.fastQC.value, dir_path)"],"metadata":{"id":"RElAhc0eY1q1","colab":{"base_uri":"https://localhost:8080/"},"executionInfo":{"status":"ok","timestamp":1689634732909,"user_tz":420,"elapsed":664,"user":{"displayName":"Elijah Spina","userId":"09538733801989465977"}},"outputId":"2b47e71e-9579-4113-deb6-723cf2f272b2"},"execution_count":5,"outputs":[{"output_type":"stream","name":"stdout","text":["Plex version (v0.8.3) up to date.\n","Temporary directory created: /tmp/3b7d47c0-412c-488d-9508-af407b047bcf3445842569\n","Reading tool config:  /fastQCdemo/fastqc.json\n","Creating IO entries from input directory:  /fastQCdemo\n","Initialized IO file at:  /tmp/3b7d47c0-412c-488d-9508-af407b047bcf3445842569/io.json\n","Initial IO JSON file CID:  QmeLbEWFvY9xCF2CmWqntE5STpiW4DwEoCpLWXFd9k9tQF\n"]}]},{"cell_type":"code","source":["from plex import plex_run\n","\n","completed_io_cid, completed_io_filepath = plex_run(initial_io_cid, PROJECT_DIR)"],"metadata":{"id":"vBEX6OHeY7JI","colab":{"base_uri":"https://localhost:8080/"},"executionInfo":{"status":"ok","timestamp":1689634747312,"user_tz":420,"elapsed":11529,"user":{"displayName":"Elijah Spina","userId":"09538733801989465977"}},"outputId":"b4b4e5a5-e9c1-4093-a738-fe31dfd40ff3"},"execution_count":6,"outputs":[{"output_type":"stream","name":"stdout","text":["Plex version (v0.8.3) up to date.\n","Created working directory:  /fastQCdemo/cd524784-4313-4e4b-ba53-72eab811aada\n","Initialized IO file at:  /fastQCdemo/cd524784-4313-4e4b-ba53-72eab811aada/io.json\n","Processing IO Entries\n","Starting to process IO entry 0 \n","Job running...\n","Bacalhau job id: e6b1fe95-6c75-4bd9-be9b-f6e632711bd1 \n","\n","Computing default go-libp2p Resource Manager limits based on:\n","    - 'Swarm.ResourceMgr.MaxMemory': \"6.8 GB\"\n","    - 'Swarm.ResourceMgr.MaxFileDescriptors': 524288\n","\n","Applying any user-supplied overrides on top.\n","Run 'ipfs swarm limit all' to see the resulting limits.\n","\n","Success processing IO entry 0 \n","Finished processing, results written to /fastQCdemo/cd524784-4313-4e4b-ba53-72eab811aada/io.json\n","Completed IO JSON CID: QmcBTfTFtT7CyyMZYZMxMpuMV2cNnyRSWCSXWg5dA1ErN9\n","2023/07/17 22:59:02 failed to sufficiently increase receive buffer size (was: 208 kiB, wanted: 2048 kiB, got: 416 kiB). See https://github.com/quic-go/quic-go/wiki/UDP-Receive-Buffer-Size for details.\n"]}]}]}