Commit 100e05f6 authored by Peter Kruczkiewicz's avatar Peter Kruczkiewicz

Merge branch 'development' into fix-612-request-uri-too-long

parents d8d67f45 3d050ee3
Changes
=======
0.20.0 to 0.21.0
----------------
* [Workflow]: Added version 0.1 of a pipeline for runing [MentaLiST](https://github.com/WGS-TB/MentaLiST) (version 0.1.3).
* [Workflow]: Added version 0.1 of a pipeline for runing Mash against the refseq database [refseq_masher](https://github.com/phac-nml/refseq_masher).
* [UI]: Fixed bug where user could not cancel the upload of a sequence file on the Sample Files page.
* [UI/Workflow]: Fixed bug where users could not submit large analyses due to an HTTP 414 "Request URI Too Long" error.
* [Developer]: Removed old gulp dependencies from the `package.json` file.
* [Developer]: Update to stable releases of `node` and `yarn`.
* [Administration]: Disabled automated SISTR results from saving to sample metadata. Also disabled retrospective results from being added during the database update. Installations that have already performed the 0.20.0 update will have their retrospective automated SISTR results automatically added to sample metadata. Installations that jump directly to 0.20.1 and above will not have this data added to sample metadata. (0.20.1)
0.19.0 to 0.20.0
----------------
* [Developer]: Fixed exception being thrown related to permission denied for updating samples when a normal user (collaborator on a project) runs the assembly pipeline (0.19.1).
......
......@@ -4,6 +4,11 @@ Upgrading
This document summarizes the environmental changes that need to be made when
upgrading IRIDA that cannot be automated.
0.20.0 to 0.21.0
----------------
* Two new pipelines, [refseq_masher](https://irida.corefacility.ca/documentation/administrator/galaxy/pipelines/refseq_masher) and [MentaLiST](https://irida.corefacility.ca/documentation/administrator/galaxy/pipelines/mentalist), are included with this release. Additional Galaxy tools will need to be installed. Please see the linked installation details for each pipeline for more information.
0.19.0 to 0.20.0
----------------
......
......@@ -11,11 +11,11 @@ The dialog that appears will provide you with a command that you can **copy** an
Copy and paste the command into a terminal window and use the username and password that you use to log in to IRIDA:
```bash
[user@waffles ~]$ ngsArchive.pl -p 4 -s 51
[user@waffles ~]$ ngsArchiveLinker.pl -p 2 -s 5
Writing files to /home/user
Enter username: user
Enter password:
Reading samples 1 from project 4
Reading samples 5 from project 2
Created 2 files for 1 samples in /home/user/Project
[user@waffles ~]$
```
......@@ -33,4 +33,4 @@ Project/
```
Importantly, the files that are stored in your directory structure are *links* and not copies of the files. The purpose of links is to reduce the use of disk space on shared resources. An unfortunate side effect of the link structure is that you **cannot** change the contents of the files.
\ No newline at end of file
Importantly, the files that are stored in your directory structure are *links* and not copies of the files. The purpose of links is to reduce the use of disk space on shared resources. An unfortunate side effect of the link structure is that you **cannot** change the contents of the files.
......@@ -113,6 +113,8 @@ Alternatively, the necessary tools can be installed manually through the followi
* [Assembly and Annotation][]
* [Assembly and Annotation Collection][]
* [SISTR Salmonella Typing][]
* [refseq_masher]
* [MentaLiST MLST][]
Link up Galaxy with IRIDA
-------------------------
......@@ -132,6 +134,8 @@ Once you have configured IRIDA to connect to Galaxy you can attempt to execute a
[SISTR Salmonella Typing]: ../pipelines/sistr/
[Assembly and Annotation]: ../pipelines/assembly-annotation/
[Assembly and Annotation Collection]: ../pipelines/assembly-annotation-collection/
[refseq_masher]: ../pipelines/refseq_masher/
[MentaLiST MLST]: ../pipelines/mentalist/
[Purging Histories and Datasets]: https://galaxyproject.org/admin/config/performance/purge-histories-and-datasets/
[Automated tools install]: https://github.com/phac-nml/irida/tree/development/packaging#automated-processupgrading
[IRIDA releases]: https://github.com/phac-nml/irida/releases
......
---
layout: default
search_title: "IRIDA MentaLiST MLST Analsyis"
description: "Install guide for the MentaLiST pipeline."
---
MentaLiST MLST Analysis
=======================
This workflow uses the software [MentaLiST][] for typing of microbial samples directly from sequence reads. The specific Galaxy tools are listed in the table below.
| Tool Name | Owner | Tool Revision | Toolshed Installable Revision | Toolshed |
|:------------------------------:|:--------:|:-------------:|:-----------------------------:|:--------------------:|
| **mentalist** | dfornika | 1d9e3950ce61 | 0 (2017-12-20) | [Galaxy Main Shed][] |
| **combine_tabular_collection** | nml | b815081988b5 | 0 (2017-02-06) | [Galaxy Main Shed][] |
## Step 1: Galaxy Conda Setup
Galaxy makes use of [Conda][conda] to automatically install some dependencies for MentaLiST. Please verify that the version of Galaxy is >= v16.01 and has been setup to use conda (by modifying the appropriate configuration settings, see [here][galaxy-config] for additional details).
## Step 2: Install Galaxy Tools
Please install all the `mentalist` Galaxy tool by logging into Galaxy, navigating to **Admin > Search Tool Shed**, searching for `mentalist` and installing the appropriate **Toolshed Installable Revision**.
The install progress can be checked by monitoring the Galaxy log files `galaxy/*.log`. On completion you should see a message of `Installed` next to the tool when going to **Admin > Manage installed tool shed repositories**.
## Step 3: Installing MentaLiST kmer Databases
MentaLiST requires an organism-specific kmer database to search against. Log in to Galaxy and navigate to **Admin > Local data**. Under **Run Data Manager Tools**, select **MentaLiST Download from pubMLST**
![mentalist-data-managers][]
Choose your kmer size. The default kmer size of 31 should work well for most applications. From the drop-down menu, select 'Salmonella enterica'.
![mentalist-download-pubmlst][]
A green result box will appear in the galaxy history once the database is complete:
![mentalist-download-pubmlst-result][]
To confirm that the database is installed, select **mentalist_databases** from the list of available Tool Data Tables:
![mentalist-data-table-list][]
Your new MentaLiST database will be listed in the table of available MentaLiST databases. If it doesn't appear, click the refresh button at the top of the table.
![mentalist-database-available][]
## Step 4: Testing Pipeline
A Galaxy workflow and some test data has been included with this documentation to verify that all tools are installed correctly. To test this pipeline, please proceed through the following steps.
1. Upload the [MentaLiST Galaxy Workflow][] by going to **Workflow > Upload or import workflow**.
2. Upload the sequence reads by going to **Analyze Data** and then clicking on the **upload files from disk** icon ![upload-icon][]. Select the [test/reads][] files. Make sure to change the **Type** of each file from **Auto-detect** to **fastqsanger**. When uploaded you should see the following in your history.
![upload-history][]
3. Construct a dataset collection of the paired-end reads by clicking the **Operations on multiple datasets** icon ![datasets-icon][]. Please check off the two **.fastq** files and then go to **For all selected... > Build List of dataset pairs**. You should see a screen that looks as follows.
![dataset-pair-screen][]
4. This should have properly paired your data and named the sample **AE014613-699860**. Enter the name of this paired dataset collection at the bottom and click **Create list**.
5. Run the uploaded workflow by clicking on **Workflow**, clicking on the name of the workflow **MentaLiST MLST v0.1 (imported from uploaded file)** and clicking **Run**. This should auto fill in the dataset collection. Ensure that an appropriate kmer database (Salmonella enterica) has been selected before running the workflow. At the very top of the screen click **Run workflow**.
6. If everything was installed correctly, you should see each of the tools run successfully (turn green). On completion this should look like.
![workflow-success][]
If you see any tool turn red, you can click on the view details icon ![view-details-icon][] for more information.
If everything was successfull then all dependencies for this pipeline have been properly installed.
[MentaLiST]: https://github.com/WGS-TB/MentaLiST
[Galaxy Main Shed]: http://toolshed.g2.bx.psu.edu/
[galaxy-config]: ../../setup#step-4-modify-configuration-file
[mentalist-data-managers]: ../test/mentalist/images/mentalist-data-managers.png
[mentalist-download-pubmlst]: ../test/mentalist/images/mentalist-download-pubmlst.png
[mentalist-download-pubmlst-result]: ../test/mentalist/images/mentalist-download-pubmlst-result.png
[mentalist-data-table-list]: ../test/mentalist/images/mentalist-data-table-list.png
[mentalist-database-available]: ../test/mentalist/images/mentalist-database-available.png
[MentaLiST Galaxy Workflow]: ../test/mentalist/mentalist.ga
[test/reads]: ../test/sistr/reads
[upload-icon]: ../test/mentalist/images/upload-icon.png
[upload-history]: ../test/mentalist/images/upload-history.png
[datasets-icon]: ../test/mentalist/images/datasets-icon.png
[dataset-pair-screen]: ../test/mentalist/images/dataset-pair-screen.png
[workflow-success]: ../test/mentalist/images/workflow-success.png
[view-details-icon]: ../test/mentalist/images/view-details-icon.png
[conda]: https://conda.io/docs/
---
layout: default
search_title: "refseq_masher"
description: "Install guide for the refseq_masher pipeline."
---
refseq_masher
=============
This workflow uses [refseq_masher] and [Mash] to find what NCBI RefSeq Genomes match or are contained in some input sequence data. The specific Galaxy tools are listed in the table below.
| Tool Name | Owner | Tool Revision | Toolshed Installable Revision | Toolshed |
|:-------------------------:|:--------:|:-------------:|:-----------------------------:|:--------------------:|
| `refseq_masher` | nml | 26df66c32861 | 0 (2018-02-15) | [Galaxy Main Shed][] |
To install these tools please proceed through the following steps.
## Step 1: Galaxy Conda Setup
Galaxy makes use of [Conda] to automatically install some dependencies for [refseq_masher]. Please verify that the version of Galaxy is >= v16.01 and has been setup to use conda (by modifying the appropriate configuration settings, see [here][galaxy-config] for additional details). A method to get [refseq_masher] to work with a Galaxy version < v16.01 is available in [FAQ/Conda dependencies].
## Step 2: Install Galaxy Tools
Please install all the Galaxy tools in the table above by logging into Galaxy, navigating to **Admin > Search and browse tool sheds**, searching for the appropriate **Tool Name** and installing the appropriate **Toolshed Installable Revision**.
The install progress can be checked by monitoring the Galaxy log files `galaxy/*.log`. On completion you should see a message of `Installed` next to the tool when going to **Admin > Manage installed tool shed repositories**.
## Step 3: Testing Pipeline
A Galaxy workflow and some test data has been included with this documentation to verify that all tools are installed correctly. To test this pipeline, please proceed through the following steps.
1. Upload the [refseq_masher Galaxy Workflow][] by going to **Workflow > Upload or import workflow**.
2. Upload the sequence reads by going to **Analyze Data** and then clicking on the **upload files from disk** icon ![upload-icon][]. Select the [test/reads][] files. Make sure to change the **Type** of each file from **Auto-detect** to **fastqsanger**. When uploaded you should see the following in your history.
![upload-history][]
3. Construct a dataset collection of the paired-end reads by clicking the **Operations on multiple datasets** icon ![datasets-icon][]. Please check off the two **.fastq** files and then go to **For all selected... > Build List of dataset pairs**. You should see a screen that looks as follows.
![dataset-pair-screen][]
4. This should have properly paired your data and named the sample **AE014613-699860**. Enter the name of this paired dataset collection at the bottom and click **Create list**.
5. Run the uploaded workflow by clicking on **Workflow**, clicking on the name of the workflow **RefSeqMasher-sequence_reads_paired-v0.1.0 (imported from uploaded file)** and clicking **Run**. This should auto fill in the dataset collection. Click **Run workflow**.
![1-workflow-run]
6. If everything was installed correctly, you should see each of the tools run successfully (turn green). On completion this should look like.
![2-workflow-output]
refseq_masher matches output:
![3-workflow-matches-output]
refseq_masher contains output:
![4-workflow-contains-output]
If you see any tool turn red, you can click on the view details icon ![view-details-icon] for more information.
If everything was successfull then all dependencies for this pipeline have been properly installed.
[refseq_masher]: https://github.com/phac-nml/refseq_masher
[Mash]: https://mash.readthedocs.io/en/latest/index.html
[refseq_masher Galaxy Workflow]: ../test/refseq_masher/refseq_masher.ga
[galaxy-config]: ../../setup#step-4-modify-configuration-file
[Galaxy Main Shed]: http://toolshed.g2.bx.psu.edu/
[upload-icon]: ../test/snvphyl/images/upload-icon.jpg
[test/reads]: ../test/sistr/reads
[upload-history]: ../test/sistr/images/upload-history.png
[datasets-icon]: ../test/snvphyl/images/datasets-icon.jpg
[dataset-pair-screen]: ../test/sistr/images/dataset-pair-screen.png
[1-workflow-run]: ../test/refseq_masher/images/1-workflow-run.png
[2-workflow-output]: ../test/refseq_masher/images/2-workflow-output.png
[3-workflow-matches-output]: ../test/refseq_masher/images/3-workflow-matches-output.png
[4-workflow-contains-output]: ../test/refseq_masher/images/4-workflow-contains-output.png
[view-details-icon]: ../test/snvphyl/images/view-details-icon.jpg
[Conda]: https://conda.io/docs/intro.html
[FAQ/Conda dependencies]: ../../../faq#installing-conda-dependencies-in-galaxy-versions--v1601
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\ No newline at end of file
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\ No newline at end of file
......@@ -271,6 +271,8 @@ Alternatively, the necessary tools can be installed manually through the followi
* [Assembly and Annotation][]
* [Assembly and Annotation Collection][]
* [SISTR Salmonella Typing][]
* [refseq_masher]
* [MentaLiST MLST][]
Each of these will step through installing the necessary tools in IRIDA. These steps will involve going to Galaxy, navigating to **Admin > Search tool sheds**, finding the appropriate tool and installing. On completion, you should be able to go to **Admin > Manage installed tools** to check the status of each tool. For a successfull install, you should see a status of `Installed`. If there is an error, you can click on each tool for more details.
......@@ -310,6 +312,8 @@ Each workflow in IRIDA is run using Galaxy, and it's possible to monitor the sta
[SISTR Salmonella Typing]: ../pipelines/sistr/
[Assembly and Annotation]: ../pipelines/assembly-annotation/
[Assembly and Annotation Collection]: ../pipelines/assembly-annotation-collection/
[refseq_masher]: ../pipelines/refseq_masher/
[MentaLiST MLST]: ../pipelines/mentalist/
[Galaxy Job Config]: https://wiki.galaxyproject.org/Admin/Config/Jobs
[saved-histories.jpg]: ../images/saved-histories.jpg
[galaxy-installed-repositories.jpg]: ../images/galaxy-installed-repositories.jpg
......
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......@@ -49,6 +49,7 @@ title: "Developer"
<li><a href="authentication">Mozilla Persona Review</a></li>
<li><a href="gmi-rest-api">GMI REST API proposal</a></li>
<li><a href="authorization/oauth2.html">OAuth2 notes</a></li>
<li><a href="clojure-repl">Clojure nREPL</a></li>
</ul>
</li>
</ul>
......
......@@ -122,33 +122,38 @@ This is an **XML** file which is used to link up a Galaxy workflow with IRIDA.
<?xml version="1.0" encoding="UTF-8"?>
<iridaWorkflow>
<id>49507566-e10c-41b2-ab6f-0fb5383be997</id>