Updated install_tutorial_requirements.sh + minor fixes (#1275)

* Install_tutorial_requirements.sh now installs tools from workflows * Extensions of LC-MS - Data Import data-library fixed * Used unzipped DOI of zenodo for iwtomics tutorial * Deleted empty workflow files * Changed revision of tools NCBI blast +, busco, custom_pro_db and goseq to latest version in workflows
galaxyproject · Feb 27, 2019 · 6eef55b · 6eef55b
1 parent b1dd99e
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diff --git a/bin/install_tutorial_requirements.sh b/bin/install_tutorial_requirements.sh
@@ -14,13 +14,24 @@ tutorial=$1
 galaxy_url=$2
 api_key=$3
 
-# install tools
-echo "Installing Tools.."
-if [ -f ${tutorial}/tools.yaml ]
+
+# install workflows and tools
+echo "Installing workflows"
+if [ -d ${tutorial}/workflows ]
 then
-    shed-tools install -g ${galaxy_url} -a ${api_key} -t ${tutorial}/tools.yaml
+    echo " - Extracting tools from workflows"
+    for w in ${tutorial}/workflows/*.ga
+    do
+        workflow-to-tools -w $w -o ${tutorial}/workflows/wftools.yaml -l $(basename ${tutorial})
+        echo " - Installing tools from workflow $(basename $w)" 
+        shed-tools install -g ${galaxy_url} -a ${api_key} -t ${tutorial}/workflows/wftools.yaml
+        rm ${tutorial}/workflows/wftools.yaml
+    done
+    echo " - Installing workflows"
+    workflow-install --publish_workflows -g ${galaxy_url} -a ${api_key} -w ${tutorial}/workflows/
+
 else
-    echo "No tools to install (no file named tools.yaml present)"
+    echo "No workflows to install (no directory named workflow present)"
 fi
 
 # install data libraries
@@ -42,15 +53,4 @@ else
     echo "No reference data to install (no file named data-manager.yaml present)"
 fi
 
-# install workflows
-echo "Installing workflows"
-if [ -d ${tutorial}/workflows ]
-then
-    workflow-install --publish_workflows -g ${galaxy_url} -a ${api_key} -w ${tutorial}/workflows/
-
-else
-    echo "No workflows to install (no directory named workflow present)"
-fi
-
-
 # install tours --> not possible via API yet
diff --git a/shared/datatypes.yaml b/shared/datatypes.yaml
@@ -17,20 +17,24 @@ fastq.gz: fastqsanger.gz
 fastq.bz: fastqsanger.bz2
 fastqsanger: fastqsanger
 fastqsanger.gz: fastqsanger.gz
-fastqsanger.bz: fastqsanger.bz2
-fna: fasta
+fastqsanger.bz: fastqsanger.bz
 fa: fasta
+fna: fasta
 fq: fastqsanger
 gbk: gbk
 gff: gff
 gff3: gff3
 gtf: gtf
 gz: gz
 html: html
+ibd: ibd
 idat: idat
+imzML: imzml
 metadata: tabular
 mgf: mgf
 mzml: mzml
+mzXML: mzxml
+obo: obo
 raw: raw
 sqlite: sqlite
 tabular: tabular

diff --git a/topics/chip-seq/tutorials/tal1-binding-site-identification/workflows/workflow.ga b/topics/chip-seq/tutorials/tal1-binding-site-identification/workflows/workflow.ga
diff --git a/...s/annotation-with-maker/data_manager.yaml → ...s/annotation-with-maker/data-manager.yaml b/...s/annotation-with-maker/data_manager.yaml → ...s/annotation-with-maker/data-manager.yaml
diff --git a/topics/genome-annotation/tutorials/annotation-with-maker/workflows/main_workflow.ga b/topics/genome-annotation/tutorials/annotation-with-maker/workflows/main_workflow.ga
diff --git a/topics/genome-annotation/tutorials/genome-annotation/workflows/workflow.ga b/topics/genome-annotation/tutorials/genome-annotation/workflows/workflow.ga
diff --git a/topics/metabolomics/tutorials/lcms-data-import/data-library.yaml b/topics/metabolomics/tutorials/lcms-data-import/data-library.yaml
@@ -17,19 +17,19 @@ items:
       items:
       - url: https://zenodo.org/api/files/bec310ad-b614-493a-8e30-5faf0f78b46e/Blanc12.mzXML
         src: url
-        ext: '# Please add a Galaxy datatype or update the shared/datatypes.yaml file'
+        ext: mzxml
         info: https://doi.org/10.5281/zenodo.1346742
       - url: https://zenodo.org/api/files/bec310ad-b614-493a-8e30-5faf0f78b46e/Blanc17.mzXML
         src: url
-        ext: '# Please add a Galaxy datatype or update the shared/datatypes.yaml file'
+        ext: mzxml
         info: https://doi.org/10.5281/zenodo.1346742
       - url: https://zenodo.org/api/files/bec310ad-b614-493a-8e30-5faf0f78b46e/HU_neg_099.mzXML
         src: url
-        ext: '# Please add a Galaxy datatype or update the shared/datatypes.yaml file'
+        ext: mzxml
         info: https://doi.org/10.5281/zenodo.1346742
       - url: https://zenodo.org/api/files/bec310ad-b614-493a-8e30-5faf0f78b46e/HU_neg_178.mzXML
         src: url
-        ext: '# Please add a Galaxy datatype or update the shared/datatypes.yaml file'
+        ext: mzxml
         info: https://doi.org/10.5281/zenodo.1346742
       - url: https://zenodo.org/api/files/bec310ad-b614-493a-8e30-5faf0f78b46e/sacuri_sampleMetadata.tsv
         src: url

diff --git a/...si-analyte-distribution/data_library.yaml → ...si-analyte-distribution/data-library.yaml b/...si-analyte-distribution/data_library.yaml → ...si-analyte-distribution/data-library.yaml
@@ -5,10 +5,10 @@ destination:
   description: Galaxy Training Network Material
   synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
 items:
-- name: The new topic
-  description: Summary
+- name: Metabolomics
+  description: Training material to analyse Metabolomics data in Galaxy - LCMS, FIAMS, GCMS and NMR<br/>Most of the training are using the tools from the <a href='http://workflow4metabolomics.org/'>Workflow4Metabolomics</a> (W4M) project.
   items:
-  - name: Title of the tutorial
+  - name: Msi analyte distribution
     items:
     - name: 'DOI: 10.5281/zenodo.484496'
       description: latest

diff --git a/topics/proteomics/tutorials/labelfree-vs-labelled/tools.yaml b/topics/proteomics/tutorials/labelfree-vs-labelled/tools.yaml
diff --git a/topics/proteomics/tutorials/labelfree-vs-labelled/workflows/workflow.ga b/topics/proteomics/tutorials/labelfree-vs-labelled/workflows/workflow.ga
diff --git a/...s/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/data-library.yaml b/...s/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/data-library.yaml
@@ -15,9 +15,9 @@ items:
       items:
       - url: https://zenodo.org/api/files/463f6b73-0c42-4be4-8b52-181a8e093abd/mouse_kidney_cut.ibd
         src: url
-        ext: '# Please add a Galaxy datatype or update the shared/datatypes.yaml file'
+        ext: ibd
         info: https://doi.org/10.5281/zenodo.1560645
       - url: https://zenodo.org/api/files/463f6b73-0c42-4be4-8b52-181a8e093abd/mouse_kidney_cut.imzML
         src: url
-        ext: '# Please add a Galaxy datatype or update the shared/datatypes.yaml file'
+        ext: imzml
         info: https://doi.org/10.5281/zenodo.1560645
diff --git a/topics/proteomics/tutorials/ntails/tools.yaml b/topics/proteomics/tutorials/ntails/tools.yaml
diff --git a/.../tutorials/proteogenomics-dbcreation/workflows/galaxy-workflow-mouse_rnaseq_dbcreation.ga b/.../tutorials/proteogenomics-dbcreation/workflows/galaxy-workflow-mouse_rnaseq_dbcreation.ga
diff --git a/...mics/tutorials/proteogenomics-dbsearch/workflows/galaxy-workflow-mouse_rnaseq_dbsearch.ga b/...mics/tutorials/proteogenomics-dbsearch/workflows/galaxy-workflow-mouse_rnaseq_dbsearch.ga
diff --git a/topics/statistics/tutorials/iwtomics/data-library.yaml b/topics/statistics/tutorials/iwtomics/data-library.yaml
@@ -11,10 +11,34 @@ items:
   items:
   - name: Interval-Wise Testing for omics data
     items:
-    - name: 'DOI: 10.5281/zenodo.1184682'
+    - name: 'DOI: 10.5281/zenodo.1288429'
       description: latest
       items:
-      - url: https://zenodo.org/api/files/d43d8e47-11fc-42de-a10f-461103f4be05/IWTomics_ETn_dataset_example.zip
+      - url: https://zenodo.org/api/files/04cbd251-fe0b-4408-9f90-e2aecd61ef09/Control.bed
+        src: url
+        ext: bed
+        info: https://zenodo.org/record/1288429
+      - url: https://zenodo.org/api/files/04cbd251-fe0b-4408-9f90-e2aecd61ef09/DESCRIPTION.txt
+        src: url
+        ext: txt
+        info: https://zenodo.org/record/1288429
+      - url: https://zenodo.org/api/files/04cbd251-fe0b-4408-9f90-e2aecd61ef09/ETn_fixed.bed
+        src: url
+        ext: bed
+        info: https://zenodo.org/record/1288429
+      - url: https://zenodo.org/api/files/04cbd251-fe0b-4408-9f90-e2aecd61ef09/features_header.tabular
+        src: url
+        ext: tabular
+        info: https://zenodo.org/record/1288429
+      - url: https://zenodo.org/api/files/04cbd251-fe0b-4408-9f90-e2aecd61ef09/IWTomics_ETn_dataset_example.zip
         src: url
         ext: zip
-        info: https://doi.org/10.5281/zenodo.1184682
+        info: https://zenodo.org/record/1288429
+      - url: https://zenodo.org/api/files/04cbd251-fe0b-4408-9f90-e2aecd61ef09/Recombination_hotspots.txt
+        src: url
+        ext: txt
+        info: https://zenodo.org/record/1288429
+      - url: https://zenodo.org/api/files/04cbd251-fe0b-4408-9f90-e2aecd61ef09/regions_header.tabular
+        src: url
+        ext: tabular
+        info: https://zenodo.org/record/1288429
diff --git a/topics/statistics/tutorials/iwtomics/tutorial.md b/topics/statistics/tutorials/iwtomics/tutorial.md
@@ -2,7 +2,7 @@
 layout: tutorial_hands_on
 
 title: "Interval-Wise Testing for omics data"
-zenodo_link: "https://doi.org/10.5281/zenodo.1184682"
+zenodo_link: "https://doi.org/10.5281/zenodo.1288429"
 questions:
   - "How to visualize high-resolution omics data in different groups of genomic regions?"
   - "How to evaluate differences in high-resolution omics data between groups of genomic regions?"

diff --git a/topics/transcriptomics/tutorials/ref-based/workflows/ref_based.ga b/topics/transcriptomics/tutorials/ref-based/workflows/ref_based.ga
@@ -2378,8 +2378,8 @@
             "type": "tool"
         },
         "39": {
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.26.0",
-            "tool_version": "1.26.0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.34.0",
+            "tool_version": "1.34.0",
             "outputs": [
                 {
                     "type": "tabular",
@@ -2427,7 +2427,7 @@
             "id": 39,
             "tool_shed_repository": {
                 "owner": "iuc",
-                "changeset_revision": "ab492df30cdf",
+                "changeset_revision": "07f6832bdd4d",
                 "name": "goseq",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
@@ -2477,7 +2477,7 @@
                 "left": 1761
             },
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.26.0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.34.0",
             "type": "tool"
         },
         "40": {
@@ -2532,4 +2532,4 @@
     },
     "annotation": "",
     "a_galaxy_workflow": "true"
-}
+}
diff --git a/topics/transcriptomics/tutorials/scrna_preprocessing/data-library.yaml b/topics/transcriptomics/tutorials/scrna_preprocessing/data-library.yaml