# \#plugin-development **URL:** https://forum.qiime2.org/tag/plugin-development/78.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt](https://forum.qiime2.org/t/processing-filtering-and-evaluating-the-silva-database-and-other-reference-sequence-data-with-rescript/15494)
**Author:** [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)\ **Replies:** 8\ **Last updated:** [February 17, 2023, 5:34pm UTC](https://forum.qiime2.org/t/processing-filtering-and-evaluating-the-silva-database-and-other-reference-sequence-data-with-rescript/15494 "2023-02-17T17:34:52Z")
:construction: Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. RESCRIPt RESCRIPt (REference Sequence annotation and CuRatIon Pipeline) is… --- ## [New Process for Tracking and Assigning Issues/Pull Requests in QIIME 2](https://forum.qiime2.org/t/new-process-for-tracking-and-assigning-issues-pull-requests-in-qiime-2/30654)
**Author:** [@lizgehret](https://forum.qiime2.org/u/lizgehret)\ **Replies:** 0\ **Last updated:** [June 28, 2024, 12:08am UTC](https://forum.qiime2.org/t/new-process-for-tracking-and-assigning-issues-pull-requests-in-qiime-2/30654 "2024-06-28T00:08:05Z")
Hi all! :wave: The QIIME 2 core development team has been testing out a new process for how we track incoming issues and pull requests, and how we can more effectively manage our community contributions along with our t… --- ## [Development of q2-pathway plugin](https://forum.qiime2.org/t/development-of-q2-pathway-plugin/30429)
**Author:** [@nsato](https://forum.qiime2.org/u/nsato)\ **Replies:** 4\ **Last updated:** [June 11, 2024, 4:03am UTC](https://forum.qiime2.org/t/development-of-q2-pathway-plugin/30429 "2024-06-11T04:03:31Z")
Hi, I have recently made a q2-pathway plugin, which is capable of: Inference of functional profiles (gene family abundance) from 16S rRNA gene sequencing data Comparison and summarization of multiple functional profil… --- ## [Missing plugins to load Artifact to run cut adapt](https://forum.qiime2.org/t/missing-plugins-to-load-artifact-to-run-cut-adapt/30138)
**Author:** [@pdv13](https://forum.qiime2.org/u/pdv13)\ **Replies:** 1\ **Last updated:** [May 7, 2024, 6:54pm UTC](https://forum.qiime2.org/t/missing-plugins-to-load-artifact-to-run-cut-adapt/30138 "2024-05-07T18:54:28Z")
Im running cutadapt, or trying and I stumped into this error: Traceback (most recent call last): File "/Users/pdv/miniconda3/envs/qiime2/lib/python3.8/site-packages/q2cli/util.py", line 492, in \_load\_input\_file artifa… --- ## [Default citations for a plugin action (function, transformer, etc)](https://forum.qiime2.org/t/default-citations-for-a-plugin-action-function-transformer-etc/29562)
**Author:** [@peterjc](https://forum.qiime2.org/u/peterjc)\ **Replies:** 6\ **Last updated:** [April 24, 2024, 4:26pm UTC](https://forum.qiime2.org/t/default-citations-for-a-plugin-action-function-transformer-etc/29562 "2024-04-24T16:26:44Z")
Consider this example (using an older version of Qiime2 as I was testing something): $ qiime dada2 --citations % use \`qiime tools citations\` on a QIIME 2 result for complete list @article{key0, author = {Callahan, Be… --- ## [Conda packaging of a new plugin](https://forum.qiime2.org/t/conda-packaging-of-a-new-plugin/29550)
**Author:** [@peterjc](https://forum.qiime2.org/u/peterjc)\ **Replies:** 6\ **Last updated:** [March 14, 2024, 5:57pm UTC](https://forum.qiime2.org/t/conda-packaging-of-a-new-plugin/29550 "2024-03-14T17:57:15Z")
I appreciate the developer docs are in flux so this question might in part just be about updating https://docs.qiime2.org/2024.2/plugins/developing/ Quoting: There are several high-level steps to registering a QIIME … --- ## [Why is my newly-registered transformer keyed by strings not types?](https://forum.qiime2.org/t/why-is-my-newly-registered-transformer-keyed-by-strings-not-types/28995)
**Author:** [@Amanda\_Birmingham](https://forum.qiime2.org/u/Amanda_Birmingham)\ **Replies:** 11\ **Last updated:** [March 12, 2024, 1:50am UTC](https://forum.qiime2.org/t/why-is-my-newly-registered-transformer-keyed-by-strings-not-types/28995 "2024-03-12T01:50:57Z")
Hi, Folks, I'm developing a plugin, and I'm starting to worry I'm going crazy :slight\_smile: I have defined and registered a new SemanticType and a new Format to go with it (see q2-pysyndna/q2\_pysyndna/\_formats\_and\_type… --- ## [Guidance on typing for functions underlying plugin actions?](https://forum.qiime2.org/t/guidance-on-typing-for-functions-underlying-plugin-actions/29368)
**Author:** [@Amanda\_Birmingham](https://forum.qiime2.org/u/Amanda_Birmingham)\ **Replies:** 3\ **Last updated:** [March 6, 2024, 4:25pm UTC](https://forum.qiime2.org/t/guidance-on-typing-for-functions-underlying-plugin-actions/29368 "2024-03-06T16:25:36Z")
Hi, All, I am working on a plugin, and I am struggling a little with the definition of the function underlying one of my plugin actions (note: NOT the action itself--I feel like I have a pretty clear idea of how to defi… --- ## [q2-amr: A Plugin for Antibiotic Resistance Gene Analysis in Qiime2](https://forum.qiime2.org/t/q2-amr-a-plugin-for-antibiotic-resistance-gene-analysis-in-qiime2/29007)
**Author:** [@Vinzent\_Risch](https://forum.qiime2.org/u/Vinzent_Risch)\ **Replies:** 0\ **Last updated:** [January 23, 2024, 4:29pm UTC](https://forum.qiime2.org/t/q2-amr-a-plugin-for-antibiotic-resistance-gene-analysis-in-qiime2/29007 "2024-01-23T16:29:18Z")
Hello Qiime2 Community! I'm excited to introduce q2-amr, a new Qiime2 plugin, designed to integrate Antibiotic Resistance Gene (ARG) analysis into Qiime2. This plugin leverages the Resistance Gene Identifier (RGI) and t… --- ## [Should developers use GitHub Actions & Library instead of (or in addition to) manually publishing to conda?](https://forum.qiime2.org/t/should-developers-use-github-actions-library-instead-of-or-in-addition-to-manually-publishing-to-conda/27437)
**Author:** [@cduvallet](https://forum.qiime2.org/u/cduvallet)\ **Replies:** 2\ **Last updated:** [September 11, 2023, 6:35pm UTC](https://forum.qiime2.org/t/should-developers-use-github-actions-library-instead-of-or-in-addition-to-manually-publishing-to-conda/27437 "2023-09-11T18:35:34Z")
Hi folks! Thanks to @mckin , q2-perc-norm is finally getting updated! I was poking around the developer docs and noticed that there's a new way to publish plugins since my last time contributing (many years ago): using… --- ## [How to output qzv from QIIME 2 plugin](https://forum.qiime2.org/t/how-to-output-qzv-from-qiime-2-plugin/26878)
**Author:** [@rouhier](https://forum.qiime2.org/u/rouhier)\ **Replies:** 1\ **Last updated:** [June 26, 2023, 4:55pm UTC](https://forum.qiime2.org/t/how-to-output-qzv-from-qiime-2-plugin/26878 "2023-06-26T16:55:55Z")
Hi there! I am developing a plugin which is a Python wrapper for a package in R that produces taxonomic abundance stacked bar plots. This plugin takes QIIME artifacts (out table, feature table, metadata, and tree) as in… --- ## [q2-krona: Plugin for creating Krona plots](https://forum.qiime2.org/t/q2-krona-plugin-for-creating-krona-plots/21294)
**Author:** [@the\_dummy](https://forum.qiime2.org/u/the_dummy)\ **Replies:** 27\ **Last updated:** [May 26, 2023, 8:15am UTC](https://forum.qiime2.org/t/q2-krona-plugin-for-creating-krona-plots/21294 "2023-05-26T08:15:55Z")
Hello everyone, I've finally got time from work and finished the plugin. :tada: Special thanks to @Nicholas\_Bokulich for suggesting making my own plugin, and @thermokarst for revision. The plugin is available at my gi… --- ## [q2-qemistree \[Errno 2\] No such file or directory: 'tmp/qiime2-archive/data/csi-output'](https://forum.qiime2.org/t/q2-qemistree-errno-2-no-such-file-or-directory-tmp-qiime2-archive-data-csi-output/18171)
**Author:** [@tinmad](https://forum.qiime2.org/u/tinmad)\ **Replies:** 9\ **Last updated:** [February 1, 2023, 12:31pm UTC](https://forum.qiime2.org/t/q2-qemistree-errno-2-no-such-file-or-directory-tmp-qiime2-archive-data-csi-output/18171 "2023-02-01T12:31:49Z")
Hello, everyone, I'm running qiime2-2019.7 in a conda environment, and I'm trying to run Qemistree using qiime2 by it's q2-qemistree plugin. (seems like not many people are using q2-qemistree). I'm following the q2-qem… --- ## [Library token for Plugin](https://forum.qiime2.org/t/library-token-for-plugin/24764)
**Author:** [@crusher083](https://forum.qiime2.org/u/crusher083)\ **Replies:** 2\ **Last updated:** [December 5, 2022, 11:01am UTC](https://forum.qiime2.org/t/library-token-for-plugin/24764 "2022-12-05T11:01:19Z")
Hello! How can I get my secret token for plugin? Cheers, Valentyn --- ## [Create an action with multiple inputs and without parameters](https://forum.qiime2.org/t/create-an-action-with-multiple-inputs-and-without-parameters/23730)
**Author:** [@Oleg](https://forum.qiime2.org/u/Oleg)\ **Replies:** 3\ **Last updated:** [August 17, 2022, 9:23am UTC](https://forum.qiime2.org/t/create-an-action-with-multiple-inputs-and-without-parameters/23730 "2022-08-17T09:23:12Z")
Hello everyone, I would like to build an action which operates on multiple input feature tables. I found this similar thread where @thermokarst suggests using the existing merge action from feature-table plugin. Howeve… --- ## [Permission errors running my developed plugin on a Google Drive FUSE mount](https://forum.qiime2.org/t/permission-errors-running-my-developed-plugin-on-a-google-drive-fuse-mount/22183)
**Author:** [@Daniela\_Perry](https://forum.qiime2.org/u/Daniela_Perry)\ **Replies:** 1\ **Last updated:** [February 15, 2022, 10:33pm UTC](https://forum.qiime2.org/t/permission-errors-running-my-developed-plugin-on-a-google-drive-fuse-mount/22183 "2022-02-15T22:33:53Z")
Hello. I am currently a rotation student in the knight lab developing a plugin that creates a visualizer. Some strange things are happening that I believe are a result of abstract Google Drive permission errors. I believ… --- ## [q2-srs: QIIME2 plugin for library size normalization by scaling with ranked subsampling (SRS)](https://forum.qiime2.org/t/q2-srs-qiime2-plugin-for-library-size-normalization-by-scaling-with-ranked-subsampling-srs/17661)
**Author:** [@vheidrich](https://forum.qiime2.org/u/vheidrich)\ **Replies:** 3\ **Last updated:** [December 6, 2021, 8:14pm UTC](https://forum.qiime2.org/t/q2-srs-qiime2-plugin-for-library-size-normalization-by-scaling-with-ranked-subsampling-srs/17661 "2021-12-06T20:14:11Z")
Hi everyone, I am happy to announce that the SRS QIIME 2 plugin is out! SRS is an alternative library size normalization tool. For details, take a look at the SRS paper or go to the @lukasbeule's topic on how SRS works… --- ## [Calling another plugin with specifications in developing a plugin](https://forum.qiime2.org/t/calling-another-plugin-with-specifications-in-developing-a-plugin/21229)
**Author:** [@the\_dummy](https://forum.qiime2.org/u/the_dummy)\ **Replies:** 2\ **Last updated:** [November 3, 2021, 6:44am UTC](https://forum.qiime2.org/t/calling-another-plugin-with-specifications-in-developing-a-plugin/21229 "2021-11-03T06:44:53Z")
Hello, I'm developing a plugin and I would like to call qiime taxa collapse and use the collapsed table as a temporary artifact. If it is not possible, I would be forced to adapt taxa methods. I would be very grateful … --- ## [New plugin (q2-srs) does not work for some users](https://forum.qiime2.org/t/new-plugin-q2-srs-does-not-work-for-some-users/17684)
**Author:** [@vheidrich](https://forum.qiime2.org/u/vheidrich)\ **Replies:** 11\ **Last updated:** [December 5, 2020, 4:24am UTC](https://forum.qiime2.org/t/new-plugin-q2-srs-does-not-work-for-some-users/17684 "2020-12-05T04:24:39Z")
Hi, I have recently posted about a new QIIME2 plugin (q2-srs). It turns out some users are facing this issue, while others are not (eg, q2-srs runs normally from a Google colab). I am currently not able to reproduce tha… --- ## [QIIME 2 plugin for ZSH](https://forum.qiime2.org/t/qiime-2-plugin-for-zsh/19865)
**Author:** [@misialq](https://forum.qiime2.org/u/misialq)\ **Replies:** 0\ **Last updated:** [June 11, 2021, 10:15am UTC](https://forum.qiime2.org/t/qiime-2-plugin-for-zsh/19865 "2021-06-11T10:15:11Z")
After having installed, uninstalled and reinstalled a number of Q2 environments I figured there was room for making that repetitive process slightly easier. As zsh is these days one of the most popular shells, I wrapped … --- ## [Problem when coding a plugin pipeline](https://forum.qiime2.org/t/problem-when-coding-a-plugin-pipeline/19729)
**Author:** [@pitaman](https://forum.qiime2.org/u/pitaman)\ **Replies:** 2\ **Last updated:** [May 30, 2021, 8:34pm UTC](https://forum.qiime2.org/t/problem-when-coding-a-plugin-pipeline/19729 "2021-05-30T20:34:24Z")
Hi, I am writing a qiime2 plugin for dbbact (dbbact.org). All the methods work, and now I am now trying to incorporate several methods into a pipeline. The output of the first method in the pipeline is defined as: Feat… --- ## [About how to output qza file](https://forum.qiime2.org/t/about-how-to-output-qza-file/18684)
**Author:** [@gcj13](https://forum.qiime2.org/u/gcj13)\ **Replies:** 1\ **Last updated:** [March 3, 2021, 5:08pm UTC](https://forum.qiime2.org/t/about-how-to-output-qza-file/18684 "2021-03-03T17:08:07Z")
I tried to write a deep neural network model into a qza file and I was wondering if there's any built-in function that might be useful. Thanks. --- ## [Designing a new plugin for qiime2](https://forum.qiime2.org/t/designing-a-new-plugin-for-qiime2/18485)
**Author:** [@gcj13](https://forum.qiime2.org/u/gcj13)\ **Replies:** 2\ **Last updated:** [February 14, 2021, 6:15pm UTC](https://forum.qiime2.org/t/designing-a-new-plugin-for-qiime2/18485 "2021-02-14T18:15:53Z")
Hello, my team is trying to work on a plugin for qiime2. We tried to use versioneer from github for the setup as other plugins do, but it keeps giving error: configparser.NoOptionError: No option 'vcs' in section: 'versi… --- ## [Discovering plugins via importlib instead of pkg\_resources](https://forum.qiime2.org/t/discovering-plugins-via-importlib-instead-of-pkg-resources/18358)
**Author:** [@cdiener](https://forum.qiime2.org/u/cdiener)\ **Replies:** 3\ **Last updated:** [February 5, 2021, 6:23pm UTC](https://forum.qiime2.org/t/discovering-plugins-via-importlib-instead-of-pkg-resources/18358 "2021-02-05T18:23:44Z")
Hi, This is kind of an exotic use case but it might be nice for teaching and making Qiime tutorials more accessible. Motivation We recently held a course teaching Qiime2 and using Google Colab. Like other (free) manage… --- ## [Code Review for a plugin?](https://forum.qiime2.org/t/code-review-for-a-plugin/17599)
**Author:** [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)\ **Replies:** 7\ **Last updated:** [December 9, 2020, 6:32pm UTC](https://forum.qiime2.org/t/code-review-for-a-plugin/17599 "2020-12-09T18:32:31Z")
Hi team, I'm not sure where else to ask for code review on a new plugin, but this seemed like a halfway decent place. I've got it working. It passes the tests and the benchmarks and works, but it would still be nice to … --- ## [Diversity statistical testing export](https://forum.qiime2.org/t/diversity-statistical-testing-export/16387)
**Author:** [@sterrettJD](https://forum.qiime2.org/u/sterrettJD)\ **Replies:** 8\ **Last updated:** [December 9, 2020, 3:03pm UTC](https://forum.qiime2.org/t/diversity-statistical-testing-export/16387 "2020-12-09T15:03:20Z")
Hi all, I've written some code to interrogate the the visualizations from q2-diversity statistical testing using the artifact API. This exports a csv containing the group significance or correlation results for every me… --- ## [SRS: Alternative tool for library size normalisation](https://forum.qiime2.org/t/srs-alternative-tool-for-library-size-normalisation/16017)
**Author:** [@lukasbeule](https://forum.qiime2.org/u/lukasbeule)\ **Replies:** 16\ **Last updated:** [December 1, 2020, 8:33pm UTC](https://forum.qiime2.org/t/srs-alternative-tool-for-library-size-normalisation/16017 "2020-12-01T20:33:53Z")
Hi everyone, I am using QIIME 2 since 2017, spend countless days with reading in the QIIME 2 forum, and highly appreciate the community support! Moreover, I am an advocate of Open Science and, thus, feel at home in the … --- ## [how to stop column cluster for metabolites in a heatmap using mmvec](https://forum.qiime2.org/t/how-to-stop-column-cluster-for-metabolites-in-a-heatmap-using-mmvec/16436)
**Author:** [@khemlalnirmalkar](https://forum.qiime2.org/u/khemlalnirmalkar)\ **Replies:** 2\ **Last updated:** [September 15, 2020, 5:03pm UTC](https://forum.qiime2.org/t/how-to-stop-column-cluster-for-metabolites-in-a-heatmap-using-mmvec/16436 "2020-09-15T17:03:31Z")
Hello Qiime2 team, I am using mmvec qiime2 plugin and i have an issue with heatmap, If you see my this 2 heatmap, the metabolites order is different, but i would like to keep in the same order, Please can you help me,… --- ## [cant save heatmap in SVG format from mmvec plugin](https://forum.qiime2.org/t/cant-save-heatmap-in-svg-format-from-mmvec-plugin/16434)
**Author:** [@khemlalnirmalkar](https://forum.qiime2.org/u/khemlalnirmalkar)\ **Replies:** 6\ **Last updated:** [September 10, 2020, 2:47am UTC](https://forum.qiime2.org/t/cant-save-heatmap-in-svg-format-from-mmvec-plugin/16434 "2020-09-10T02:47:29Z")
Hello, I am using mmvec qiime2 plugin and i have an issue, If you see my heatmap, log scale and metabolite names are interfering with each other. Since qiime2 view is giving me only PDF format to save, i can't edit it.… --- ## [Juggle between semantic types and view types?](https://forum.qiime2.org/t/juggle-between-semantic-types-and-view-types/15332)
**Author:** [@lea\_si](https://forum.qiime2.org/u/lea_si)\ **Replies:** 2\ **Last updated:** [June 12, 2020, 1:45pm UTC](https://forum.qiime2.org/t/juggle-between-semantic-types-and-view-types/15332 "2020-06-12T13:45:29Z")
Dear all, I am currently trying to develop my first QIIME2 plugin, and I admit having a hard time juggling between data types. I'd appreciate any guidance from someone more experienced with the API :slight\_smile: My ai… [Next page](https://forum.qiime2.org/tag/plugin-development/78.md?match_all_tags=true&page=1&tags%5B%5D=plugin-development)