Skip to content

Commit 3a1e2c4

Browse files
bernt-matthiasbernt-matthias
committed
version 0.75.27
1 parent 3f33aca commit 3a1e2c4

35 files changed

+329
-164
lines changed

‎HISTORY.rst

Lines changed: 16 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,16 @@
33
History
44
-------
55

6-
.. to_doc
6+
---------------------
7+
0.75.27 (2025-03-03)
8+
---------------------
9+
* Remove usage of `defaults` conda channel (thanks to `@bernt-matthias`_).
10+
`Pull Request 1487`_
11+
* Add category "Geo Science" (thanks to `@bernt-matthias`_). `Pull Request 1483`_
12+
* Bump requirements for galaxy packages to 24.2 (thanks to `@jdavcs`_). `Pull
13+
Request 1491`_
14+
* Use python 3.13 for deploymen (thanks to `@bernt-matthias`_). `Pull Request 1488`_
15+
* Fix repository category update (thanks to `@mvdbeek`_). `Pull Request 1481`_
716

817
---------------------
918
0.75.26 (2024-09-24)
@@ -2156,6 +2165,11 @@ History
21562165
tools - and more experimental features involving Docker and Homebrew. 7d07782_
21572166

21582167
.. github_links
2168+
.. _Pull Request 1487: https://github.com/galaxyproject/planemo/pull/1487
2169+
.. _Pull Request 1483: https://github.com/galaxyproject/planemo/pull/1483
2170+
.. _Pull Request 1491: https://github.com/galaxyproject/planemo/pull/1491
2171+
.. _Pull Request 1488: https://github.com/galaxyproject/planemo/pull/1488
2172+
.. _Pull Request 1481: https://github.com/galaxyproject/planemo/pull/1481
21592173
.. _Pull Request 1474: https://github.com/galaxyproject/planemo/pull/1474
21602174
.. _Pull Request 1452: https://github.com/galaxyproject/planemo/pull/1452
21612175
.. _Pull Request 1473: https://github.com/galaxyproject/planemo/pull/1473
@@ -3113,3 +3127,4 @@ History
31133127
.. _@Delphine-L: https://github.com/Delphine-L
31143128
.. _@elichad: https://github.com/elichad
31153129
.. _@pavanvidem: https://github.com/pavanvidem
3130+
.. _@jdavcs: https://github.com/jdavcs

‎docs/commands/autoupdate.rst

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -143,7 +143,7 @@ Auto-update tool requirements by checking against Conda and updating if newer ve
143143
packages.
144144
--conda_auto_init / --no_conda_auto_init
145145
Conda dependency resolution for Galaxy will
146-
auto install conda itself using miniconda if
146+
auto install conda itself using miniforge if
147147
not availabe on conda_prefix.
148148
--simultaneous_uploads / --no_simultaneous_uploads
149149
When uploading files to Galaxy for tool or

‎docs/commands/conda_install.rst

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,7 @@ Install conda packages for tool requirements.
3434
and debugging.
3535
--conda_auto_init / --no_conda_auto_init
3636
Conda dependency resolution for Galaxy will
37-
auto install conda itself using miniconda if
37+
auto install conda itself using miniforge if
3838
not availabe on conda_prefix.
3939
--help Show this message and exit.
4040

‎docs/commands/mull.rst

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@ target tool(s).
3131
subdirectories.
3232
--mulled_conda_version TEXT Install a specific version of Conda before
3333
running the command, by default the version
34-
that comes with the continuumio miniconda3
34+
that comes with the continuumio miniforge
3535
image will be used under Linux and under Mac
3636
OS X Conda will be upgraded to to work around
3737
a bug in 4.2.

‎docs/commands/mulled_init.rst

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -22,7 +22,7 @@ be pre-installed in an environment using this command.
2222

2323
--mulled_conda_version TEXT Install a specific version of Conda before
2424
running the command, by default the version that
25-
comes with the continuumio miniconda3 image will
25+
comes with the continuumio miniforge image will
2626
be used under Linux and under Mac OS X Conda will
2727
be upgraded to to work around a bug in 4.2.
2828
--mulled_namespace TEXT Build a mulled image with the specified namespace

‎docs/commands/run.rst

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -107,7 +107,7 @@ Planemo command for running tools and jobs.
107107
packages.
108108
--conda_auto_init / --no_conda_auto_init
109109
Conda dependency resolution for Galaxy will
110-
auto install conda itself using miniconda if
110+
auto install conda itself using miniforge if
111111
not availabe on conda_prefix.
112112
--simultaneous_uploads / --no_simultaneous_uploads
113113
When uploading files to Galaxy for tool or

‎docs/commands/serve.rst

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -135,7 +135,7 @@ Galaxy instance.
135135
packages.
136136
--conda_auto_init / --no_conda_auto_init
137137
Conda dependency resolution for Galaxy will
138-
auto install conda itself using miniconda if
138+
auto install conda itself using miniforge if
139139
not availabe on conda_prefix.
140140
--simultaneous_uploads / --no_simultaneous_uploads
141141
When uploading files to Galaxy for tool or

‎docs/commands/shed_init.rst

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,7 @@ to manage repositories in a Galaxy Tool Shed.
2929
--remote_repository_url TEXT Specify repository remote_repository_url for
3030
.shed.yml.
3131
--homepage_url TEXT Specify repository homepage_url for .shed.yml.
32-
--category [Assembly|Astronomy|ChIP-seq|Climate Analysis|CLIP-seq|Combinatorial Selections|Computational chemistry|Constructive Solid Geometry|Convert Formats|Data Export|Data Managers|Data Source|Ecology|Entomology|Epigenetics|Fasta Manipulation|Fastq Manipulation|Flow Cytometry Analysis|Genome annotation|Genome editing|Genome-Wide Association Study|Genomic Interval Operations|GIS|Graphics|Imaging|InteractiveTools|Machine Learning|Materials science|Metabolomics|Metagenomics|Micro-array Analysis|Molecular Dynamics|Muon spectroscopy|Nanopore|Next Gen Mappers|NLP|Ontology Manipulation|Phylogenetics|Proteomics|RNA|SAM|Sequence Analysis|Single Cell|Spatial Omics|Statistics|Structural Materials Analysis|Synthetic Biology|Systems Biology|Text Manipulation|Tool Dependency Packages|Tool Generators|Transcriptomics|Variant Analysis|Visualization|Web Services]
32+
--category [Assembly|Astronomy|ChIP-seq|Climate Analysis|CLIP-seq|Combinatorial Selections|Computational chemistry|Constructive Solid Geometry|Convert Formats|Data Export|Data Managers|Data Source|Ecology|Entomology|Epigenetics|Fasta Manipulation|Fastq Manipulation|Flow Cytometry Analysis|Genome annotation|Genome editing|Genome-Wide Association Study|Genomic Interval Operations|Geo Science|GIS|Graphics|Imaging|InteractiveTools|Machine Learning|Materials science|Metabolomics|Metagenomics|Micro-array Analysis|Molecular Dynamics|Muon spectroscopy|Nanopore|Next Gen Mappers|NLP|Ontology Manipulation|Phylogenetics|Proteomics|RNA|SAM|Sequence Analysis|Single Cell|Spatial Omics|Statistics|Structural Materials Analysis|Synthetic Biology|Systems Biology|Text Manipulation|Tool Dependency Packages|Tool Generators|Transcriptomics|Variant Analysis|Visualization|Web Services]
3333
Specify repository category for .shed.yml (may
3434
specify multiple).
3535
--owner TEXT Tool Shed repository owner (username).

‎docs/commands/shed_serve.rst

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -143,7 +143,7 @@ logged into and explored interactively.
143143
packages.
144144
--conda_auto_init / --no_conda_auto_init
145145
Conda dependency resolution for Galaxy will
146-
auto install conda itself using miniconda if
146+
auto install conda itself using miniforge if
147147
not availabe on conda_prefix.
148148
--simultaneous_uploads / --no_simultaneous_uploads
149149
When uploading files to Galaxy for tool or

‎docs/commands/shed_test.rst

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -124,7 +124,7 @@ install these artifacts, and run the tool tests for these commands.
124124
packages.
125125
--conda_auto_init / --no_conda_auto_init
126126
Conda dependency resolution for Galaxy will
127-
auto install conda itself using miniconda if
127+
auto install conda itself using miniforge if
128128
not availabe on conda_prefix.
129129
--simultaneous_uploads / --no_simultaneous_uploads
130130
When uploading files to Galaxy for tool or

0 commit comments

Comments
 (0)