fix repository URLs (#5016)

* fix repository URLs

* fix homepage URL

Co-authored-by: Nicola Soranzo <[email protected]>

* replace all remote_repository_url

for i in $(grep -l "remote_repository_url:.*" data_managers/ tools tool_collections --include ".shed.*" -r)
do
    d=$(dirname $i);
    sed -i -e "s@^remote_repository_url:.*@remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/$d@" $i
done

---------

Co-authored-by: Nicola Soranzo <[email protected]>

Author: bernt-matthias

data_managers/data_manager_bowtie2_index_builder/.shed.yml

@@ -6,5 +6,5 @@ long_description: |
     Data Manager for building bowtie2 indexes
 name: data_manager_bowtie2_index_builder
 owner: devteam
-remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_bowtie2_index_builder
 type: unrestricted

data_managers/data_manager_bowtie_index_builder/.shed.yml

@@ -10,5 +10,5 @@ long_description: |
   GB for paired-end).
 name: data_manager_bowtie_index_builder
 owner: iuc
-remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_bowtie_index_builder
 type: unrestricted

data_managers/data_manager_build_amrfinderplus/.shed.yml

@@ -5,6 +5,6 @@ long_description: |
   This data manager update to the latest databases for amrfinderplus or bakta tools
 name: amrfinderplus_data_manager_build
 owner: iuc
-remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus
 type: unrestricted
 homepage_url: "https://github.com/ncbi/amr"

data_managers/data_manager_build_bakta_database/.shed.yml

@@ -6,6 +6,6 @@ long_description: |
   and updates the bakta data table.
 name: data_manager_bakta
 owner: iuc
-remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bakta_database
 type: unrestricted
 homepage_url: https://github.com/oschwengers/bakta

data_managers/data_manager_build_bracken_database/.shed.yml

@@ -10,5 +10,5 @@ long_description: |
   can estimate abundance of species within a sample).
 name: data_manager_build_bracken_database
 owner: iuc
-remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database
 type: unrestricted

data_managers/data_manager_build_coreprofiler/.shed.yml

@@ -4,7 +4,7 @@ description: "Download scheme containing the list of official alleles curated by
 homepage_url: "https://gitlab.com/ifb-elixirfr/abromics/coreprofiler"
 long_description: |
     Download scheme containing the list of official alleles curated by its reference platform (such as BIGSdb for Klebsiella pneumoniae or Listeria, Enterobase for E. coli, PubMLST for Staphylococcus aureus, etc) for CoreProfiler. 
-remote_repository_url: "https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_coreprofiler"
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_coreprofiler
 type: unrestricted
 categories:
 - Data Managers

data_managers/data_manager_build_kma_index/.shed.yml

@@ -11,5 +11,5 @@ long_description: |
   attributes, based on our users demands.
 name: data_manager_build_kma_index
 owner: iuc
-remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kma_index
 type: unrestricted

data_managers/data_manager_build_kraken2_database/.shed.yml

@@ -14,5 +14,5 @@ long_description: |
   and a novel classification algorithm.
 name: data_manager_build_kraken2_database
 owner: iuc
-remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database
 type: unrestricted

data_managers/data_manager_build_kraken_database/.shed.yml

@@ -14,5 +14,5 @@ long_description: |
   and a novel classification algorithm.
 name: data_manager_build_kraken_database
 owner: devteam
-remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken_database
 type: unrestricted

data_managers/data_manager_build_staramr/.shed.yml

@@ -4,7 +4,7 @@ description: "Download the Resfinder, Pointfinder and Plasmidfinder databases fo
 homepage_url: "https://github.com/phac-nml/staramr"
 long_description: |
     Download the Resfinder, Pointfinder and Plasmidfinder databases for starAMR using the commits corresponding to the versions of the different databases. 
-remote_repository_url: "https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_staramr"
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_staramr
 type: unrestricted
 categories:
 - Data Managers