Removed a few other mentions of IRIDA Galaxy toolshed and fixed some …

…broken links

doc/administrator/galaxy/pipelines/assembly-annotation-collection/index.md

@@ -68,7 +68,6 @@ If everything was successful then all dependencies for this pipeline have been p
 [Prokka]: http://www.vicbioinformatics.com/software.prokka.shtml
 [QUAST]: http://quast.sourceforge.net/quast.html
 [Galaxy Main Shed]: http://toolshed.g2.bx.psu.edu/
-[IRIDA Toolshed]: https://irida.corefacility.ca/galaxy-shed
 [Assembly Annotation Collection Galaxy Workflow]: ../test/assembly-annotation-collection/assembly-annotation-collection.ga
 [upload-icon]: ../test/snvphyl/images/upload-icon.jpg
 [test/reads]: ../test/assembly-annotation/reads
@@ -80,5 +79,5 @@ If everything was successful then all dependencies for this pipeline have been p
 [FAQ]: ../../../faq/#tbl2asn-out-of-date
 [conda]: https://conda.io/docs/intro.html
 [bioconda]: https://bioconda.github.io/
-[FAQ/Conda dependencies]: ../../../faq#installing-conda-dependencies-in-galaxy-versions--v1601
+[FAQ/Conda dependencies]: ../../../faq#4-installing-conda-dependencies-in-galaxy-versions--v1601
 [conda environment]: https://conda.io/docs/user-guide/tasks/manage-environments.html#saving-environment-variables

doc/administrator/galaxy/pipelines/assembly-annotation/index.md

@@ -78,6 +78,6 @@ If everything was successful then all dependencies for this pipeline have been p
 [FAQ]: ../../../faq/#tbl2asn-out-of-date
 [conda]: https://conda.io/docs/intro.html
 [bioconda]: https://bioconda.github.io/
-[FAQ/Conda dependencies]: ../../../faq#installing-conda-dependencies-in-galaxy-versions--v1601
+[FAQ/Conda dependencies]: ../../../faq#4-installing-conda-dependencies-in-galaxy-versions--v1601
 [conda environment]: https://conda.io/docs/user-guide/tasks/manage-environments.html#saving-environment-variables
 [GALAXY_MEMORY_MB]: https://planemo.readthedocs.io/en/latest/writing_advanced.html#developing-for-clusters-galaxy-slots-galaxy-memory-mb-and-galaxy-memory-mb-per-slot

doc/administrator/galaxy/pipelines/refseq_masher/index.md

@@ -69,12 +69,10 @@ If everything was successfull then all dependencies for this pipeline have been
 [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
+[FAQ/Conda dependencies]: ../../../faq#4-installing-conda-dependencies-in-galaxy-versions--v1601

doc/administrator/galaxy/pipelines/sistr/index.md

@@ -73,6 +73,6 @@ If everything was successfull then all dependencies for this pipeline have been
 [conda]: https://conda.io/docs/intro.html
 [bioconda]: https://bioconda.github.io/
 [sistr_cmd]: https://github.com/peterk87/sistr_cmd
-[FAQ/Conda dependencies]: ../../../faq#installing-conda-dependencies-in-galaxy-versions--v1601
+[FAQ/Conda dependencies]: ../../../faq#4-installing-conda-dependencies-in-galaxy-versions--v1601
 [conda environment]: https://conda.io/docs/user-guide/tasks/manage-environments.html#saving-environment-variables
 [GALAXY_MEMORY_MB]: https://planemo.readthedocs.io/en/latest/writing_advanced.html#developing-for-clusters-galaxy-slots-galaxy-memory-mb-and-galaxy-memory-mb-per-slot

doc/developer/tools/pipelines/index.md

@@ -11,7 +11,7 @@ This document describes the necessary steps for integrating new pipelines into I
 
 # 1. Introduction
 
-Pipelines in IRIDA take as input data managed by IRIDA and run through a collection of tools to produce some meaningful result.  Pipelines are implemented as a [Galaxy Workflow][] and executed using an instance of [Galaxy][] that has been setup for IRIDA.  Pipelines are versioned and are stored and distributed either along with the IRIDA software, or as a separate plugin compiled into a Java JAR file.  Tools used by a pipeline are versioned and are stored and distributed using [Galaxy Toolsheds][].  In particular, the [Galaxy Main Toolshed][] and the [IRIDA Toolshed][] are used to store and distribute tools for a pipeline.
+Pipelines in IRIDA take as input data managed by IRIDA and run through a collection of tools to produce some meaningful result.  Pipelines are implemented as a [Galaxy Workflow][] and executed using an instance of [Galaxy][] that has been setup for IRIDA.  Pipelines are versioned and are stored and distributed either along with the IRIDA software, or as a separate plugin compiled into a Java JAR file.  Tools used by a pipeline are versioned and are stored and distributed using [Galaxy Toolsheds][].  In particular, the [Galaxy Main Toolshed][] is used to store and distribute tools for a pipeline.
 
 ![irida-pipelines][]
 
@@ -435,7 +435,6 @@ DEBUG ca.corefacility.bioinformatics.irida.config.services.IridaPluginConfig:45
 [Galaxy]: http://galaxyproject.org/
 [Galaxy Toolsheds]: https://wiki.galaxyproject.org/ToolShed
 [Galaxy Main Toolshed]: https://toolshed.g2.bx.psu.edu/
-[IRIDA Toolshed]: https://irida.corefacility.ca/galaxy-shed
 [galaxy-workflow-editor]: images/galaxy-workflow-editor.png
 [irida-pipelines]: images/irida-pipelines.png
 [Galaxy Workflow]: https://wiki.galaxyproject.org/Learn/AdvancedWorkflow