From 31b02f0d407deffd0165fcb85fe3974c73196292 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Tue, 17 Sep 2024 15:44:13 +0200 Subject: [PATCH 1/3] fix-db-selection --- tools/gtdbtk/gtdbtk_classify_wf.xml | 4 +-- .../gtdbtk_database_versioned.loc.test | 26 +++++++++++++++++++ tools/gtdbtk/tool_data_table_conf.xml.test | 3 ++- 3 files changed, 30 insertions(+), 3 deletions(-) create mode 100644 tools/gtdbtk/test-data/gtdbtk_database_versioned.loc.test diff --git a/tools/gtdbtk/gtdbtk_classify_wf.xml b/tools/gtdbtk/gtdbtk_classify_wf.xml index 31d997cc6b9..2e896ba6b66 100644 --- a/tools/gtdbtk/gtdbtk_classify_wf.xml +++ b/tools/gtdbtk/gtdbtk_classify_wf.xml @@ -37,9 +37,9 @@ $advanced.force ]]> - + - + diff --git a/tools/gtdbtk/test-data/gtdbtk_database_versioned.loc.test b/tools/gtdbtk/test-data/gtdbtk_database_versioned.loc.test new file mode 100644 index 00000000000..6805759ec5c --- /dev/null +++ b/tools/gtdbtk/test-data/gtdbtk_database_versioned.loc.test @@ -0,0 +1,26 @@ +# This is a sample file distributed with Galaxy that enables tools +# to use a directory of GTDB-Tk databases. The gtdbtk_databases.loc +# file has this format (longer white space characters are TAB characters): +# +# +# +# So, for example, if you have the gtdbtk 202 stored in +# /depot/data2/galaxy/gtdbtk/202/, +# then the gtdbtk_databases.loc entry would look like this: +# +# release202 gtdbtk database release 202 /depot/data2/galaxy/gtdbtk/release202 +# +# and your /depot/data2/galaxy/gtdbtk/release202 directory +# would contain GTDB-Tk database files for release 202, sommething like this: +# +#drwxr-sr-x 3 gvk G-824019 4096 Apr 20 2021 fastani/ +#-rw-r--r-- 1 gvk G-824019 4810764 Apr 22 2021 manifest.tsv +#drwxr-sr-x 4 gvk G-824019 4096 Apr 21 2021 markers/ +#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 masks/ +#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 metadata/ +#drwxr-sr-x 2 gvk G-824019 4096 Apr 21 2021 mrca_red/ +#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 msa/ +#drwxr-sr-x 4 gvk G-824019 4096 Apr 21 2021 pplacer/ +#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 radii/ +#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 taxonomy/ +gtdbtk214 GTDB-Tk database 214 ${__HERE__}/gtdbtk214/ diff --git a/tools/gtdbtk/tool_data_table_conf.xml.test b/tools/gtdbtk/tool_data_table_conf.xml.test index cd2a1af37b9..bf76fbd6a35 100644 --- a/tools/gtdbtk/tool_data_table_conf.xml.test +++ b/tools/gtdbtk/tool_data_table_conf.xml.test @@ -1,7 +1,8 @@ + value, name, version, path - +
From 0d9bb1d971906f636705aa82f3196c9d5d09dc34 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Tue, 17 Sep 2024 15:44:43 +0200 Subject: [PATCH 2/3] remove old test loc --- .../test-data/gtdbtk_database_versioned.loc | 26 ------------------- 1 file changed, 26 deletions(-) delete mode 100644 tools/gtdbtk/test-data/gtdbtk_database_versioned.loc diff --git a/tools/gtdbtk/test-data/gtdbtk_database_versioned.loc b/tools/gtdbtk/test-data/gtdbtk_database_versioned.loc deleted file mode 100644 index 06709a3fb3c..00000000000 --- a/tools/gtdbtk/test-data/gtdbtk_database_versioned.loc +++ /dev/null @@ -1,26 +0,0 @@ -# This is a sample file distributed with Galaxy that enables tools -# to use a directory of GTDB-Tk databases. The gtdbtk_databases.loc -# file has this format (longer white space characters are TAB characters): -# -# -# -# So, for example, if you have the gtdbtk 202 stored in -# /depot/data2/galaxy/gtdbtk/202/, -# then the gtdbtk_databases.loc entry would look like this: -# -# release202 gtdbtk database release 202 /depot/data2/galaxy/gtdbtk/release202 -# -# and your /depot/data2/galaxy/gtdbtk/release202 directory -# would contain GTDB-Tk database files for release 202, sommething like this: -# -#drwxr-sr-x 3 gvk G-824019 4096 Apr 20 2021 fastani/ -#-rw-r--r-- 1 gvk G-824019 4810764 Apr 22 2021 manifest.tsv -#drwxr-sr-x 4 gvk G-824019 4096 Apr 21 2021 markers/ -#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 masks/ -#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 metadata/ -#drwxr-sr-x 2 gvk G-824019 4096 Apr 21 2021 mrca_red/ -#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 msa/ -#drwxr-sr-x 4 gvk G-824019 4096 Apr 21 2021 pplacer/ -#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 radii/ -#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 taxonomy/ -gtdbtk214 GTDB-Tk database v214 ${__HERE__}/gtdbtk214/ From 2f8cb60f7eb14094ff2ad46a243b071a450b794e Mon Sep 17 00:00:00 2001 From: paulzierep Date: Tue, 24 Sep 2024 09:53:05 +0200 Subject: [PATCH 3/3] bump and column name based filter --- tools/gtdbtk/gtdbtk_classify_wf.xml | 2 +- tools/gtdbtk/macros.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/gtdbtk/gtdbtk_classify_wf.xml b/tools/gtdbtk/gtdbtk_classify_wf.xml index 2e896ba6b66..b9b0f7e6382 100644 --- a/tools/gtdbtk/gtdbtk_classify_wf.xml +++ b/tools/gtdbtk/gtdbtk_classify_wf.xml @@ -39,7 +39,7 @@ $advanced.force - + diff --git a/tools/gtdbtk/macros.xml b/tools/gtdbtk/macros.xml index dc490f0b61c..585aaedc6c7 100644 --- a/tools/gtdbtk/macros.xml +++ b/tools/gtdbtk/macros.xml @@ -1,6 +1,6 @@ 2.3.2 - 4 + 5 22.05