| Name | AmpliconSuiteAggregator JSON |
| Version |
2
JSON |
| download |
| home_page | None |
| Summary | Aggregator tool for multiple Amplicon Architect outputs |
| upload_time | 2024-08-21 07:35:22 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | ---------------------------------------------------------------- *** GENEPATTERN LICENSE AGREEMENT *** ---------------------------------------------------------------- GenePattern is distributed under the following BSD-style license: Copyright (c) 2003-2022 Regents of the University of California. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names of the Regents of the University of California nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED AS IS. REGENTS OF THE UNIVERSITY OF CALIFORNIA MAKE NO EXPRESS OR IMPLIED REPRESENTATIONS OR WARRANTIES OF ANY KIND REGARDING THE SOFTWARE AND COPYRIGHT, INCLUDING, BUT NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, CONFORMITY WITH ANY DOCUMENTATION, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. IN NO EVENT SHALL REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE COPYRIGHT HOLDERS, OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF, HAVE REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF SUCH DAMAGE. If, by operation of law or otherwise, any of the aforementioned warranty disclaimers are determined inapplicable, your sole remedy, regardless of the form of action, including, but not limited to, negligence and strict liability, shall be replacement of the software with an updated version if one exists. |
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# Amplicon Suite Aggregator
## Description
Aggregates the results from AmpliconSuite
- Takes in zip files (completed results of individual or grouped Amplicon Suite runs)
- Aggregates results
- Packages results into a new file
- Outputs an aggregated .html and .csv file of results.
- Result file (in .tar.gz) is the aggregated results of all individual AmpliconSutie runs. It can be directly loaded onto AmpliconRepository.
- Can also take additional files along with the upload, provided the directory they are in contains a file named `AUX_DIR`.
## Parameters available on GenePattern Server
- Available at: https://genepattern.ucsd.edu/gp/pages/index.jsf?lsid=urn:lsid:genepattern.org:module.analysis:00429:4.1
- *Amplicon Architect Results* (required)
- Compressed (.tar.gz, .zip) files of the results from individual or grouped Amplicon Architect runs.
- *project_name* (required)
- Prefix for output .tar.gz. Result will be named: *output_prefix*.tar.gz
- *Amplicon Repository Email*
- If wanting to directly transfer results to AmpliconRepository.org, please enter your email.
- *run amplicon classifier*
- Option for users to re-run Amplicon Classifier.
- *reference genome*
- Reference genome used for Amplicon Architect results in the input.
- *upload only*
- If 'Yes', then skip aggregation / classification and upload file to AmpliconRepository as is.
- *name map*
- A two column file providing the current identifier for each sample (col 1) and a replacement name (col 2). Enables batch renaming of samples.
## Installation
- Option 1: Git Clone
- Step 1: `git clone https://github.com/genepattern/AmpliconSuiteAggregator.git`
- Step 2: Install python package dependencies from list below.
- **If running into dependency issues, please use the docker methods.**
- Option 2: Docker
- Step 1: `docker pull genepattern/amplicon-suite-aggregator`
## Dependencies
- List of python package dependencies used: intervaltree, matplotlib, numpy, pandas, Pillow, requests, scipy, urllib3
## Options when running locally
### Amplicon Suite Aggregator related options
- `-flist` / `--filelist`: Text file with files to use (one per line)
- Create an `input_list.txt` file in this format where each line is a filepath to compressed aa_results:
<img width="269" alt="image" src="https://github.com/genepattern/AmpliconSuiteAggregator/assets/43209173/cca8c8af-a58f-4290-a8a8-4dbe82e5941e">
- Use this file as the input to the `-flist` flag.
- `--files`: List of files or directories to use. Can specify multiple paths of (.tar.gz, .zip) of Amplicon Architect results.
- `-o` / `--output_name`: Output Prefix. Will be used as project name for Amplicon Repository upload.
- `--name_map`: A two column file providing the current identifier for each sample (col 1) and a replacement name (col 2). Enables batch renaming of samples.
- `-c` / `--run_classifier` (Yes, No): If 'Yes', then run Amplicon Classifier on AA samples. If Amplicon Classifier results are already included in inputs, then they will be removed and samples will be re-classified.
- `--ref` (hg19, GRCh37, GRCh38, GRCh38_viral, mm10): Reference genome name used for alignment, one of hg19, GRCh37, GRCh38, GRCh38_viral, or mm10.
### AmpliconRepository related options
- `-u` / `--username`: Email address for Amplicon Repository. If specified, will trigger an attempt to upload the aggregated file to AmpliconRepository.org.
- `--upload_only` (Yes, No): If 'Yes', then skip aggregation / classification and upload file to AmpliconRepository as is.
- `-s` / `--server` (dev, prod, local-debug): Which server to send results to. Accepts 'dev' or 'prod' or 'local-debug'. 'prod' is what most users want. 'dev' and 'local-debug' are for development and debugging.
## How to run
- If using local CLI:
- Running aggregator: `python3 /path/to/AmpliconSuiteAggregator/path/src/AmpliconSuiteAggregator.py **options**`
- Using API to upload directly to AmpliconRepository **without aggregation**: `python3 /path/to/AmpliconSuiteAggregator/path/src/AmpliconSuiteAggregator.py --files /path/to/aggregated/file.tar.gz -o projname -u your.amplicon.repository.username@gmail.com --upload_only Yes -s prod`
- Log into Amplicon Repository, you should see a new project with the output prefix you specified.
- If using Docker:
- To Running aggregator:
1. `docker run --rm -it -v PATH/TO/INPUTS/FOLDER:/inputs/ genepattern/amplicon-suite-aggregator python3 /opt/genepatt/AmpliconSuiteAggregator.py **options**`
- Using API to upload directly to AmpliconRepository **without aggregation**:
1. `docker run --rm -it -v PATH/TO/INPUTS/FOLDER:/inputs/ genepattern/amplicon-suite-aggregator python3 /opt/genepatt/AmpliconSuiteAggregator.py -flist /path/to/input_list.txt -u YOUR_AMPLICON_REPOSITORY_EMAIL -o projname -u your.amplicon.repository.username@gmail.com --upload_only Yes -s prod`
2. Log into Amplicon Repository, you should see a new project with the output prefix you specified.
## Programming Language
- Python
## Contact
For any issues
- Edwin Huang, edh021@cloud.ucsd.edu
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"description": "# Amplicon Suite Aggregator\n\n## Description\nAggregates the results from AmpliconSuite\n - Takes in zip files (completed results of individual or grouped Amplicon Suite runs)\n - Aggregates results\n - Packages results into a new file\n - Outputs an aggregated .html and .csv file of results. \n - Result file (in .tar.gz) is the aggregated results of all individual AmpliconSutie runs. It can be directly loaded onto AmpliconRepository.\n - Can also take additional files along with the upload, provided the directory they are in contains a file named `AUX_DIR`.\n \n## Parameters available on GenePattern Server\n - Available at: https://genepattern.ucsd.edu/gp/pages/index.jsf?lsid=urn:lsid:genepattern.org:module.analysis:00429:4.1\n - *Amplicon Architect Results* (required)\n - Compressed (.tar.gz, .zip) files of the results from individual or grouped Amplicon Architect runs.\n - *project_name* (required)\n - Prefix for output .tar.gz. Result will be named: *output_prefix*.tar.gz\n - *Amplicon Repository Email*\n - If wanting to directly transfer results to AmpliconRepository.org, please enter your email.\n - *run amplicon classifier*\n - Option for users to re-run Amplicon Classifier.\n - *reference genome*\n - Reference genome used for Amplicon Architect results in the input.\n - *upload only*\n - If 'Yes', then skip aggregation / classification and upload file to AmpliconRepository as is.\n - *name map*\n - A two column file providing the current identifier for each sample (col 1) and a replacement name (col 2). Enables batch renaming of samples.\n\n\n## Installation\n - Option 1: Git Clone\n - Step 1: `git clone https://github.com/genepattern/AmpliconSuiteAggregator.git`\n - Step 2: Install python package dependencies from list below.\n - **If running into dependency issues, please use the docker methods.** \n - Option 2: Docker\n - Step 1: `docker pull genepattern/amplicon-suite-aggregator`\n\n## Dependencies\n - List of python package dependencies used: intervaltree, matplotlib, numpy, pandas, Pillow, requests, scipy, urllib3 \n\n## Options when running locally\n### Amplicon Suite Aggregator related options\n - `-flist` / `--filelist`: Text file with files to use (one per line)\n - Create an `input_list.txt` file in this format where each line is a filepath to compressed aa_results:\n <img width=\"269\" alt=\"image\" src=\"https://github.com/genepattern/AmpliconSuiteAggregator/assets/43209173/cca8c8af-a58f-4290-a8a8-4dbe82e5941e\">\n\n - Use this file as the input to the `-flist` flag.\n - `--files`: List of files or directories to use. Can specify multiple paths of (.tar.gz, .zip) of Amplicon Architect results.\n - `-o` / `--output_name`: Output Prefix. Will be used as project name for Amplicon Repository upload.\n - `--name_map`: A two column file providing the current identifier for each sample (col 1) and a replacement name (col 2). Enables batch renaming of samples.\n - `-c` / `--run_classifier` (Yes, No): If 'Yes', then run Amplicon Classifier on AA samples. If Amplicon Classifier results are already included in inputs, then they will be removed and samples will be re-classified.\n - `--ref` (hg19, GRCh37, GRCh38, GRCh38_viral, mm10): Reference genome name used for alignment, one of hg19, GRCh37, GRCh38, GRCh38_viral, or mm10.\n\n### AmpliconRepository related options\n - `-u` / `--username`: Email address for Amplicon Repository. If specified, will trigger an attempt to upload the aggregated file to AmpliconRepository.org.\n - `--upload_only` (Yes, No): If 'Yes', then skip aggregation / classification and upload file to AmpliconRepository as is.\n - `-s` / `--server` (dev, prod, local-debug): Which server to send results to. Accepts 'dev' or 'prod' or 'local-debug'. 'prod' is what most users want. 'dev' and 'local-debug' are for development and debugging.\n\n## How to run\n - If using local CLI:\n - Running aggregator: `python3 /path/to/AmpliconSuiteAggregator/path/src/AmpliconSuiteAggregator.py **options**`\n - Using API to upload directly to AmpliconRepository **without aggregation**: `python3 /path/to/AmpliconSuiteAggregator/path/src/AmpliconSuiteAggregator.py --files /path/to/aggregated/file.tar.gz -o projname -u your.amplicon.repository.username@gmail.com --upload_only Yes -s prod`\n - Log into Amplicon Repository, you should see a new project with the output prefix you specified. \n\n - If using Docker:\n - To Running aggregator: \n 1. `docker run --rm -it -v PATH/TO/INPUTS/FOLDER:/inputs/ genepattern/amplicon-suite-aggregator python3 /opt/genepatt/AmpliconSuiteAggregator.py **options**`\n - Using API to upload directly to AmpliconRepository **without aggregation**:\n 1. `docker run --rm -it -v PATH/TO/INPUTS/FOLDER:/inputs/ genepattern/amplicon-suite-aggregator python3 /opt/genepatt/AmpliconSuiteAggregator.py -flist /path/to/input_list.txt -u YOUR_AMPLICON_REPOSITORY_EMAIL -o projname -u your.amplicon.repository.username@gmail.com --upload_only Yes -s prod`\n 2. Log into Amplicon Repository, you should see a new project with the output prefix you specified. \n \n## Programming Language\n - Python\n\n## Contact\nFor any issues\n - Edwin Huang, edh021@cloud.ucsd.edu\n",
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"license": "---------------------------------------------------------------- *** GENEPATTERN LICENSE AGREEMENT *** ---------------------------------------------------------------- GenePattern is distributed under the following BSD-style license: Copyright (c) 2003-2022 Regents of the University of California. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the names of the Regents of the University of California nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED AS IS. REGENTS OF THE UNIVERSITY OF CALIFORNIA MAKE NO EXPRESS OR IMPLIED REPRESENTATIONS OR WARRANTIES OF ANY KIND REGARDING THE SOFTWARE AND COPYRIGHT, INCLUDING, BUT NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, CONFORMITY WITH ANY DOCUMENTATION, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. IN NO EVENT SHALL REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE COPYRIGHT HOLDERS, OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF, HAVE REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF SUCH DAMAGE. If, by operation of law or otherwise, any of the aforementioned warranty disclaimers are determined inapplicable, your sole remedy, regardless of the form of action, including, but not limited to, negligence and strict liability, shall be replacement of the software with an updated version if one exists. ",
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