From b9feea216497855acfab694f4f3258b45572811e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Fri, 19 Jan 2018 13:35:45 +0100 Subject: [PATCH 1/3] Fixing data manager --- config/data_managers.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/config/data_managers.yaml b/config/data_managers.yaml index f4f7201..08673f0 100644 --- a/config/data_managers.yaml +++ b/config/data_managers.yaml @@ -12,7 +12,7 @@ data_managers: - qiime_taxonomy - qiime_trees - - id: toolshed.g2.bx.psu.edu/repos/rnateam/data_manager_sortmerna_database_downloader/data_manager_sortmerna_download/2.1b.0 + - id: toolshed.g2.bx.psu.edu/repos/rnateam/data_manager_sortmerna_database_downloader/data_manager_sortmerna_download/2.1b.1 params: - '': '{{ item }}' items: @@ -29,7 +29,7 @@ data_managers: data_table_reload: - metaphlan2_database - - id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_humann2_database_downloader/data_manager_humann2_download/0.9.9 + - id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_humann2_database_downloader/data_manager_humann2_download/0.11.1.0 # HUMAnN2 database: Nucleotide database: full chocophlan params: - 'db|database': 'chocophlan' @@ -39,7 +39,7 @@ data_managers: data_table_reload: - humann2_nucleotide_database - - id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_humann2_database_downloader/data_manager_humann2_download/0.9.9 + - id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_humann2_database_downloader/data_manager_humann2_download/0.11.1.0 # HUMAnN2 database: Protein database: full uniref50 params: - 'db|database': 'uniref' @@ -49,7 +49,7 @@ data_managers: data_table_reload: - humann2_protein_database - #- id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_humann2_database_downloader/data_manager_humann2_download/0.9.9 + #- id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_humann2_database_downloader/data_manager_humann2_download/0.11.1.0 # # HUMAnN2 database: Protein database: full uniref90 # params: # - 'db|database': 'uniref' From 99daf533991ea83209bf5dd0342578309542ad76 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Fri, 19 Jan 2018 14:24:54 +0100 Subject: [PATCH 2/3] Replace origin image --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index c3effa8..3d7c06c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,5 @@ # Galaxy - ASaiM -FROM bgruening/galaxy-stable:17.09 +FROM quay.io/bgruening/galaxy:17.09 MAINTAINER Bérénice Batut, berenice.batut@gmail.com From 6ea1217eea65b5338b733e921633b66598e60ec2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Sun, 21 Jan 2018 10:48:28 +0100 Subject: [PATCH 3/3] Fix link to shtgun wf --- config/workflows/shotgun_workflow.ga | 919 +-------------------------- 1 file changed, 1 insertion(+), 918 deletions(-) diff --git a/config/workflows/shotgun_workflow.ga b/config/workflows/shotgun_workflow.ga index 6098312..b7a9ea5 100644 --- 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