update data library files

Author: shiltemann

topics/assembly/tutorials/assembly-decontamination/data-library.yaml

@@ -1,19 +1,24 @@
 ---
+zenodo_id: '13367433'
 destination:
   type: library
   name: GTN - Material
   description: Galaxy Training Network Material
   synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
 items:
-- name: New topic
-  description: Topic summary
+- name: Assembly
+  description: DNA sequence data has become an indispensable tool for Molecular Biology
+    & Evolutionary Biology. Study in these fields now require a genome sequence to
+    work from. We call this a 'Reference Sequence.' We need to build a reference for
+    each species. We do this by Genome Assembly. De novo Genome Assembly is the process
+    of reconstructing the original DNA sequence from the fragment reads alone.
   items:
   - name: Decontamination of a genome assembly
     items:
     - name: 'DOI: 10.5281/zenodo.13367433'
       description: latest
-      items: 
-        - info: https://doi.org/10.5281/zenodo.13367433
-          url: https://zenodo.org/records/13367433/files/Contaminated_assembly.fasta
-          ext: fasta
-          src: url
+      items:
+      - url: https://zenodo.org/record/13367433/files/Contaminated_assembly.fasta
+        src: url
+        ext: fasta
+        info: https://doi.org/10.5281/zenodo.13367433

topics/assembly/tutorials/assembly-quality-control/data-library.yaml

@@ -1,4 +1,5 @@
 ---
+zenodo_id: '6947782'
 destination:
   type: library
   name: GTN - Material
@@ -17,19 +18,19 @@ items:
     - name: 'DOI: 10.5281/zenodo.6947782'
       description: latest
       items:
-      - url: https://zenodo.org/api/files/51d69187-a6ad-43d5-8abc-21c8b5dc652c/GCA_000146045.2_genomic.fna
+      - url: https://zenodo.org/record/6947782/files/GCA_000146045.2_genomic.fna
         src: url
         ext: fasta
         info: https://doi.org/10.5281/zenodo.6947782
-      - url: https://zenodo.org/api/files/51d69187-a6ad-43d5-8abc-21c8b5dc652c/Scerevisiae-INSC1019.flye.30x.fa
+      - url: https://zenodo.org/record/6947782/files/Scerevisiae-INSC1019.flye.30x.fa
         src: url
         ext: fasta
         info: https://doi.org/10.5281/zenodo.6947782
-      - url: https://zenodo.org/api/files/51d69187-a6ad-43d5-8abc-21c8b5dc652c/Scerevisiae-INSC1019.hifiasm.30x.fa
+      - url: https://zenodo.org/record/6947782/files/SRR13577847_subreads.30x.fastq.gz
         src: url
-        ext: fasta
+        ext: fastqsanger.gz
         info: https://doi.org/10.5281/zenodo.6947782
-      - url: https://zenodo.org/api/files/51d69187-a6ad-43d5-8abc-21c8b5dc652c/SRR13577847_subreads.30x.fastq.gz
+      - url: https://zenodo.org/record/6947782/files/Scerevisiae-INSC1019.hifiasm.30x.fa
         src: url
-        ext: fastqsanger.gz
+        ext: fasta
         info: https://doi.org/10.5281/zenodo.6947782

topics/assembly/tutorials/assembly-with-preprocessing/data-library.yaml

@@ -1,4 +1,5 @@
 ---
+zenodo_id: '3732359'
 destination:
   type: library
   name: GTN - Material
@@ -18,39 +19,39 @@ items:
     - name: 'DOI: 10.5281/zenodo.3732359'
       description: latest
       items:
-      - url: https://zenodo.org/api/files/28b4a623-35a4-428d-a3dd-77d26f9eb4b6/SRR10902284_ONT.fq.gz
+      - url: https://zenodo.org/record/3732359/files/SRR10903401_r1.fq.gz
         src: url
-        ext: fastq.gz
+        ext: fastqsanger.gz
         info: https://doi.org/10.5281/zenodo.3732359
-      - url: https://zenodo.org/api/files/28b4a623-35a4-428d-a3dd-77d26f9eb4b6/SRR10903401_r1.fq.gz
+      - url: https://zenodo.org/record/3732359/files/SRR10903401_r2.fq.gz
         src: url
-        ext: fastq.gz
+        ext: fastqsanger.gz
         info: https://doi.org/10.5281/zenodo.3732359
-      - url: https://zenodo.org/api/files/28b4a623-35a4-428d-a3dd-77d26f9eb4b6/SRR10903401_r2.fq.gz
+      - url: https://zenodo.org/record/3732359/files/SRR10948474_ONT.fq.gz
         src: url
-        ext: fastq.gz
+        ext: fastqsanger.gz
         info: https://doi.org/10.5281/zenodo.3732359
-      - url: https://zenodo.org/api/files/28b4a623-35a4-428d-a3dd-77d26f9eb4b6/SRR10903402_r1.fq.gz
+      - url: https://zenodo.org/record/3732359/files/SRR10903402_r1.fq.gz
         src: url
-        ext: fastq.gz
+        ext: fastqsanger.gz
         info: https://doi.org/10.5281/zenodo.3732359
-      - url: https://zenodo.org/api/files/28b4a623-35a4-428d-a3dd-77d26f9eb4b6/SRR10903402_r2.fq.gz
+      - url: https://zenodo.org/record/3732359/files/SRR10948550_ONT.fq.gz
         src: url
-        ext: fastq.gz
+        ext: fastqsanger.gz
         info: https://doi.org/10.5281/zenodo.3732359
-      - url: https://zenodo.org/api/files/28b4a623-35a4-428d-a3dd-77d26f9eb4b6/SRR10948474_ONT.fq.gz
+      - url: https://zenodo.org/record/3732359/files/SRR10902284_ONT.fq.gz
         src: url
-        ext: fastq.gz
+        ext: fastqsanger.gz
         info: https://doi.org/10.5281/zenodo.3732359
-      - url: https://zenodo.org/api/files/28b4a623-35a4-428d-a3dd-77d26f9eb4b6/SRR10948550_ONT.fq.gz
+      - url: https://zenodo.org/record/3732359/files/SRR10903402_r2.fq.gz
         src: url
-        ext: fastq.gz
+        ext: fastqsanger.gz
         info: https://doi.org/10.5281/zenodo.3732359
-      - url: https://zenodo.org/api/files/28b4a623-35a4-428d-a3dd-77d26f9eb4b6/SRR10971381_r1.fq.gz
+      - url: https://zenodo.org/record/3732359/files/SRR10971381_r1.fq.gz
         src: url
-        ext: fastq.gz
+        ext: fastqsanger.gz
         info: https://doi.org/10.5281/zenodo.3732359
-      - url: https://zenodo.org/api/files/28b4a623-35a4-428d-a3dd-77d26f9eb4b6/SRR10971381_r2.fq.gz
+      - url: https://zenodo.org/record/3732359/files/SRR10971381_r2.fq.gz
         src: url
-        ext: fastq.gz
+        ext: fastqsanger.gz
         info: https://doi.org/10.5281/zenodo.3732359

topics/assembly/tutorials/chloroplast-assembly/data-library.yaml

@@ -1,31 +1,36 @@
 ---
+zenodo_id: '3567224'
 destination:
   type: library
   name: GTN - Material
   description: Galaxy Training Network Material
   synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
 items:
 - name: Assembly
-  description: Genome assembly
+  description: DNA sequence data has become an indispensable tool for Molecular Biology
+    & Evolutionary Biology. Study in these fields now require a genome sequence to
+    work from. We call this a 'Reference Sequence.' We need to build a reference for
+    each species. We do this by Genome Assembly. De novo Genome Assembly is the process
+    of reconstructing the original DNA sequence from the fragment reads alone.
   items:
   - name: Chloroplast genome assembly
     items:
     - name: 'DOI: 10.5281/zenodo.3567224'
       description: latest
       items:
-      - info: http://doi.org/10.5281/zenodo.3567224
-        url: https://zenodo.org/record/3567224/files/sweet-potato-chloroplast-illumina-reduced.fastq
-        ext: fastqsanger
+      - url: https://zenodo.org/record/3567224/files/sweet-potato-chloroplast-nanopore-tiny.fastq
         src: url
-      - info: http://doi.org/10.5281/zenodo.3567224
-        url: https://zenodo.org/record/3567224/files/sweet-potato-chloroplast-nanopore-reduced.fastq
         ext: fastqsanger
+        info: https://doi.org/10.5281/zenodo.3567224
+      - url: https://zenodo.org/record/3567224/files/sweet-potato-chloroplast-nanopore-reduced.fastq
         src: url
-      - info: http://doi.org/10.5281/zenodo.3567224
-        url: https://zenodo.org/record/3567224/files/sweet-potato-chloroplast-illumina-tiny.fastq
         ext: fastqsanger
+        info: https://doi.org/10.5281/zenodo.3567224
+      - url: https://zenodo.org/record/3567224/files/sweet-potato-chloroplast-illumina-tiny.fastq
         src: url
-      - info: http://doi.org/10.5281/zenodo.3567224
-        url: https://zenodo.org/record/3567224/files/sweet-potato-chloroplast-nanopore-tiny.fastq
         ext: fastqsanger
+        info: https://doi.org/10.5281/zenodo.3567224
+      - url: https://zenodo.org/record/3567224/files/sweet-potato-chloroplast-illumina-reduced.fastq
         src: url
+        ext: fastqsanger
+        info: https://doi.org/10.5281/zenodo.3567224

topics/assembly/tutorials/debruijn-graph-assembly/data-library.yaml

@@ -1,4 +1,5 @@
 ---
+zenodo_id: '582600'
 destination:
   type: library
   name: GTN - Material
@@ -17,11 +18,23 @@ items:
     - name: 'DOI: 10.5281/zenodo.582600'
       description: latest
       items:
-      - url: https://zenodo.org/api/files/287966da-5411-4f79-8cfb-0ffa84d0d6cc/mutant_R1.fastq
+      - url: https://zenodo.org/record/582600/files/mutant_R1.fastq
         src: url
         ext: fastqsanger
         info: https://doi.org/10.5281/zenodo.582600
-      - url: https://zenodo.org/api/files/287966da-5411-4f79-8cfb-0ffa84d0d6cc/mutant_R2.fastq
+      - url: https://zenodo.org/record/582600/files/wildtype.gbk
+        src: url
+        ext: gbk
+        info: https://doi.org/10.5281/zenodo.582600
+      - url: https://zenodo.org/record/582600/files/mutant_R2.fastq
         src: url
         ext: fastqsanger
         info: https://doi.org/10.5281/zenodo.582600
+      - url: https://zenodo.org/record/582600/files/wildtype.gff
+        src: url
+        ext: gff
+        info: https://doi.org/10.5281/zenodo.582600
+      - url: https://zenodo.org/record/582600/files/wildtype.fna
+        src: url
+        ext: fasta
+        info: https://doi.org/10.5281/zenodo.582600

topics/assembly/tutorials/ecoli_comparison/data-library.yaml

@@ -1,4 +1,5 @@
 ---
+zenodo_id: '3382053'
 destination:
   type: library
   name: GTN - Material
@@ -14,20 +15,42 @@ items:
   items:
   - name: Making sense of a newly assembled genome
     items:
-    - name: 'DOI: 10.5281/zenodo.1306128'
+    - name: 'DOI: 10.5281/zenodo.3382053'
       description: latest
       items:
-      - url: https://zenodo.org/api/files/0a441269-78e5-4c70-b313-b10cb798907a/Ecoli_C_assembly.fna
+      - url: https://zenodo.org/record/3382053/files/CP020543.1.fasta.gz
         src: url
-        ext: fasta
-        info: https://doi.org/10.5281/zenodo.1306128
-  - name: E. coli C assembly
-    description: Training material for analysis of new assemblies
-    items:
-    - name: 'DOI: 10.5281/zenodo.1257429'
-      description: latest
-      items:
-      - url: https://zenodo.org/record/1306128/files/Ecoli_C_assembly.fna
+        ext: fasta.gz
+        info: https://doi.org/10.5281/zenodo.3382053
+      - url: https://zenodo.org/record/3382053/files/LT906474.1.genes.tsv
+        src: url
+        ext: tsv
+        info: https://doi.org/10.5281/zenodo.3382053
+      - url: https://zenodo.org/record/3382053/files/LT906474.1.fasta.gz
+        src: url
+        ext: fasta.gz
+        info: https://doi.org/10.5281/zenodo.3382053
+      - url: https://zenodo.org/record/3382053/files/inline-supplementary-material-7.tsv
+        src: url
+        ext: tsv
+        info: https://doi.org/10.5281/zenodo.3382053
+      - url: https://zenodo.org/record/3382053/files/genomes_proks.txt
+        src: url
+        ext: txt
+        info: https://doi.org/10.5281/zenodo.3382053
+      - url: https://zenodo.org/record/3382053/files/E._coli_C.fasta.gz
+        src: url
+        ext: fasta.gz
+        info: https://doi.org/10.5281/zenodo.3382053
+      - url: https://zenodo.org/record/3382053/files/CP024090.1.genes.tsv
+        src: url
+        ext: tsv
+        info: https://doi.org/10.5281/zenodo.3382053
+      - url: https://zenodo.org/record/3382053/files/CP024090.1.fasta.gz
+        src: url
+        ext: fasta.gz
+        info: https://doi.org/10.5281/zenodo.3382053
+      - url: https://zenodo.org/record/3382053/files/CP020543.1.genes.tsv
         src: url
-        ext: fasta
-        info: https://zenodo.org/record/1257429
+        ext: tsv
+        info: https://doi.org/10.5281/zenodo.3382053

topics/assembly/tutorials/general-introduction/data-library.yaml

@@ -1,4 +1,5 @@
 ---
+zenodo_id: '582600'
 destination:
   type: library
   name: GTN - Material
@@ -12,20 +13,28 @@ items:
     each species. We do this by Genome Assembly. De novo Genome Assembly is the process
     of reconstructing the original DNA sequence from the fragment reads alone.
   items:
-  - name: Introduction to Genome Assembly
+  - name: An Introduction to Genome Assembly
     items:
     - name: 'DOI: 10.5281/zenodo.582600'
       description: latest
       items:
-      - url: https://zenodo.org/api/files/287966da-5411-4f79-8cfb-0ffa84d0d6cc/mutant_R1.fastq
+      - url: https://zenodo.org/record/582600/files/mutant_R1.fastq
         src: url
         ext: fastqsanger
         info: https://doi.org/10.5281/zenodo.582600
-      - url: https://zenodo.org/api/files/287966da-5411-4f79-8cfb-0ffa84d0d6cc/mutant_R2.fastq
+      - url: https://zenodo.org/record/582600/files/wildtype.gbk
+        src: url
+        ext: gbk
+        info: https://doi.org/10.5281/zenodo.582600
+      - url: https://zenodo.org/record/582600/files/mutant_R2.fastq
         src: url
         ext: fastqsanger
         info: https://doi.org/10.5281/zenodo.582600
-      - url: https://zenodo.org/api/files/287966da-5411-4f79-8cfb-0ffa84d0d6cc/wildtype.fna
+      - url: https://zenodo.org/record/582600/files/wildtype.gff
+        src: url
+        ext: gff
+        info: https://doi.org/10.5281/zenodo.582600
+      - url: https://zenodo.org/record/582600/files/wildtype.fna
         src: url
         ext: fasta
         info: https://doi.org/10.5281/zenodo.582600

topics/assembly/tutorials/largegenome/data-library.yaml

@@ -1,32 +1,36 @@
 ---
+zenodo_id: '7055935'
 destination:
   type: library
   name: GTN - Material
   description: Galaxy Training Network Material
   synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
 items:
 - name: Assembly
-  description: Genome assembly
+  description: DNA sequence data has become an indispensable tool for Molecular Biology
+    & Evolutionary Biology. Study in these fields now require a genome sequence to
+    work from. We call this a 'Reference Sequence.' We need to build a reference for
+    each species. We do this by Genome Assembly. De novo Genome Assembly is the process
+    of reconstructing the original DNA sequence from the fragment reads alone.
   items:
   - name: Large genome assembly and polishing
     items:
     - name: 'DOI: 10.5281/zenodo.7055935'
       description: latest
       items:
-      - info: https://doi.org/10.5281/zenodo.7055935
-        url: https://zenodo.org/record/7055935/files/Eucalyptus_subsample_ten_pc_nano_SRR7153076.fastq.gz
-        ext: fastq.gz
+      - url: https://zenodo.org/record/7055935/files/Eucalyptus_subsample_ten_pc_SRR7153045_R1.fastq.gz
         src: url
-      - info: https://doi.org/10.5281/zenodo.7055935
-        url: https://zenodo.org/record/7055935/files/Eucalyptus_subsample_ten_pc_SRR7153045_R1.fastq.gz
-        ext: fastq.gz
+        ext: fastqsanger.gz
+        info: https://doi.org/10.5281/zenodo.7055935
+      - url: https://zenodo.org/record/7055935/files/Eucalyptus_subsample_ten_pc_SRR7153045_R2.fastq.gz
         src: url
-      - info: https://doi.org/10.5281/zenodo.7055935
-        url: https://zenodo.org/record/7055935/files/Eucalyptus_subsample_ten_pc_SRR7153045_R2.fastq.gz
-        ext: fastq.gz
+        ext: fastqsanger.gz
+        info: https://doi.org/10.5281/zenodo.7055935
+      - url: https://zenodo.org/record/7055935/files/Eucalyptus_subsample_ten_pc_nano_SRR7153076.fastq.gz
         src: url
-      - info: https://doi.org/10.5281/zenodo.7055935
-        url: https://zenodo.org/record/7055935/files/Ref_genome_Arabidopsis.fasta
-        ext: fasta
+        ext: fastqsanger.gz
+        info: https://doi.org/10.5281/zenodo.7055935
+      - url: https://zenodo.org/record/7055935/files/Ref_genome_Arabidopsis.fasta
         src: url
-
+        ext: fasta
+        info: https://doi.org/10.5281/zenodo.7055935

topics/assembly/tutorials/mitochondrion-assembly/data-library.yaml

@@ -1,4 +1,5 @@
 ---
+zenodo_id: '13345315'
 destination:
   type: library
   name: GTN - Material

topics/assembly/tutorials/mrsa-illumina/data-library.yaml

@@ -1,4 +1,5 @@
 ---
+zenodo_id: '10669812'
 destination:
   type: library
   name: GTN - Material
@@ -12,20 +13,21 @@ items:
     each species. We do this by Genome Assembly. De novo Genome Assembly is the process
     of reconstructing the original DNA sequence from the fragment reads alone.
   items:
-  - name: Genome Assembly of MRSA using Illumina MiSeq Data
+  - name: Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq
+      Data
     items:
     - name: 'DOI: 10.5281/zenodo.10669812'
       description: latest
       items:
-      - url: https://zenodo.org/api/files/52e04e0d-851d-42ff-8dd9-932b38cb8ca8/DRR187559_1.fastqsanger.bz2
+      - url: https://zenodo.org/record/10669812/files/DRR187567.fastq.bz2
         src: url
         ext: fastqsanger.bz2
         info: https://doi.org/10.5281/zenodo.10669812
-      - url: https://zenodo.org/api/files/52e04e0d-851d-42ff-8dd9-932b38cb8ca8/DRR187559_2.fastqsanger.bz2
+      - url: https://zenodo.org/record/10669812/files/DRR187559_2.fastqsanger.bz2
         src: url
         ext: fastqsanger.bz2
         info: https://doi.org/10.5281/zenodo.10669812
-      - url: https://zenodo.org/api/files/52e04e0d-851d-42ff-8dd9-932b38cb8ca8/DRR187567.fastq.bz2
+      - url: https://zenodo.org/record/10669812/files/DRR187559_1.fastqsanger.bz2
         src: url
-        ext: fastq.bz2
+        ext: fastqsanger.bz2
         info: https://doi.org/10.5281/zenodo.10669812