Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

update config for 24.1 #1225

Merged
merged 7 commits into from
Jul 10, 2024
Merged

update config for 24.1 #1225

Show file tree
Hide file tree
Changes from 2 commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
0648121
update config for 24.1
bgruening Jun 4, 2024
da7ed17
Merge branch 'master' into release_24.1
bgruening Jun 4, 2024
ba2adab
add file_source_template config file
bgruening Jun 4, 2024
bb01c94
Add templates for object store and file sources, update playbook, and…
sanjaysrikakulam Jul 5, 2024
0b49201
Update galaxy commit id to 24.1 release
sanjaysrikakulam Jul 5, 2024
246db72
Disable file source and object store config for now in 24.1 rollout
sanjaysrikakulam Jul 9, 2024
605cde4
Undo the commit bb01c94ca30589914217ea6cfb6941bdce6273fc
sanjaysrikakulam Jul 10, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
28 changes: 22 additions & 6 deletions files/galaxy/config/datatypes_conf.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
<datatype extension="gfa2" auto_compressed_types="gz" type="galaxy.datatypes.text:Gfa2" mimetype="text/plain" display_in_upload="true"/>
<datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true"/>
<datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true"/>
<datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format. Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/>
<datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="A pairwise alignment format." description_url="https://genome.ucsc.edu/goldenPath/help/axt.html"/>
<datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/>
<datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
<converter file="bam_to_bai.xml" target_datatype="bai"/>
Expand Down Expand Up @@ -225,9 +225,9 @@
<display file="igv/interval_as_bed.xml" inherit="true"/>
</datatype>
<datatype extension="jellyfish" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true" description="Jellyfish database files are k-mer counts in binary format with a readable head. They are operated on and converted to human-readable text through jellyfish commands." />
<datatype extension="ktab" type="galaxy.datatypes.binary:Binary" subclass="true" description="A table of canonical k‑mers and their counts for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
<datatype extension="hist" type="galaxy.datatypes.binary:Binary" subclass="true" description="A binary histogram file of kmers and frequencies for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
<datatype extension="prof" type="galaxy.datatypes.binary:Binary" subclass="true" description="Read profile file for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
<datatype extension="fastk_ktab" type="galaxy.datatypes.binary:Binary" subclass="true" description="A table of canonical k‑mers and their counts for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
<datatype extension="fastk_hist" type="galaxy.datatypes.binary:Binary" subclass="true" description="A binary histogram file of kmers and frequencies for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
<datatype extension="fastk_prof" type="galaxy.datatypes.binary:Binary" subclass="true" description="Read profile file for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
<datatype extension="npy" type="galaxy.datatypes.binary:Numpy" description="Standard format for saving numpy arrays" display_in_upload="true" description_url="https://numpy.org/devdocs/reference/generated/numpy.lib.format.html"/>

<!-- ISA data types -->
Expand Down Expand Up @@ -395,6 +395,7 @@
<datatype extension="star" type="galaxy.datatypes.images:Star" display_in_upload="true" />
<datatype extension="peff" type="galaxy.datatypes.proteomics:PEFF" display_in_upload="true" />
<datatype extension="toml" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
<datatype extension="colab.tar" auto_compressed_types="gz" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
<!-- End Proteomics Datatypes -->
<!-- FlowCytometry -->
<datatype extension="fcs" type="galaxy.datatypes.flow:FCS" mimetype="application/octet-stream" display_in_upload="true" description="A FCS binary sequence file with a '.fcs' file extension." />
Expand Down Expand Up @@ -949,10 +950,16 @@
<!-- media datatypes -->
<datatype extension="wav" type="galaxy.datatypes.media:Wav" display_in_upload="true" mimetype="audio/wav"/>
<datatype extension="mp3" type="galaxy.datatypes.media:Mp3" display_in_upload="true" mimetype="audio/mp3"/>
<datatype extension="ogg" type="galaxy.datatypes.media:Ogg" display_in_upload="true" mimetype="audio/ogg"/>
<datatype extension="wma" type="galaxy.datatypes.media:Wma" display_in_upload="true" mimetype="audio/x-ms-wma"/>
<datatype extension="mkv" type="galaxy.datatypes.media:Mkv" display_in_upload="true" mimetype="video/mkv"/>
<datatype extension="mp4" type="galaxy.datatypes.media:Mp4" display_in_upload="true" mimetype="video/mp4"/>
<datatype extension="flv" type="galaxy.datatypes.media:Flv" display_in_upload="true" mimetype="video/flv"/>
<datatype extension="webm" type="galaxy.datatypes.media:Webm" display_in_upload="true" mimetype="video/webm"/>
<datatype extension="mpg" type="galaxy.datatypes.media:Mpg" display_in_upload="true" mimetype="video/mpeg"/>
<datatype extension="mov" type="galaxy.datatypes.media:Mov" display_in_upload="true" mimetype="video/quicktime"/>
<datatype extension="avi" type="galaxy.datatypes.media:Avi" display_in_upload="true" mimetype="video/x-msvideo"/>
<datatype extension="wmv" type="galaxy.datatypes.media:Wmv" display_in_upload="true" mimetype="video/x-ms-wmv"/>
<!-- speech datatypes -->
<datatype extension="textgrid" type="galaxy.datatypes.speech:TextGrid" display_in_upload="true" mimetype="text/plain"/>
<datatype extension="par" type="galaxy.datatypes.speech:BPF" display_in_upload="true" mimetype="text/plain-bas"/>
Expand Down Expand Up @@ -1006,7 +1013,8 @@
<datatype extension="shp" type="galaxy.datatypes.gis:Shapefile" mimetype="application/octet-stream" display_in_upload="true" description="geospatial vector data format for geographic information system"/>
<!-- Flexible Image Transport System (FITS) used in Astronomy https://fits.gsfc.nasa.gov/ https://fits.gsfc.nasa.gov/rfc4047.txt -->
<datatype extension="fits" type="galaxy.datatypes.binary:FITS" mimetype="application/octet-stream" display_in_upload="true" description="Flexible Image Transport System (FITS) used in Astronomy"/>
<datatype extension="chain" type="galaxy.datatypes.chain:Chain" display_in_upload="true"/>
<datatype extension="chain" type="galaxy.datatypes.chain:Chain" display_in_upload="true" description_url="https://genome.ucsc.edu/goldenPath/help/chain.html"/>
<datatype extension="ucsc.net" type="galaxy.datatypes.chain:Net" display_in_upload="true" description_url="https://genome.ucsc.edu/goldenPath/help/net.html"/>
</registration>
<sniffers>
<!--
Expand Down Expand Up @@ -1102,7 +1110,7 @@
<sniffer type="galaxy.datatypes.binary:Edr"/>
<sniffer type="galaxy.datatypes.binary:Vel"/>
<sniffer type="galaxy.datatypes.binary:Xlsx"/>
<sniffer type="galaxy.datatypes.binary:Numpy"/>
<sniffer type="galaxy.datatypes.binary:Numpy"/>
<sniffer type="galaxy.datatypes.qiime2:QIIME2Metadata"/>
<sniffer type="galaxy.datatypes.qiime2:QIIME2Artifact"/>
<sniffer type="galaxy.datatypes.qiime2:QIIME2Visualization"/>
Expand All @@ -1111,6 +1119,7 @@
<sniffer type="galaxy.datatypes.annotation:Augustus"/>
<sniffer type="galaxy.datatypes.xml:Owl"/>
<sniffer type="galaxy.datatypes.chain:Chain"/>
<sniffer type="galaxy.datatypes.chain:Net"/>
<sniffer type="galaxy.datatypes.triples:Rdf"/>
<sniffer type="galaxy.datatypes.blast:BlastXml"/>
<sniffer type="galaxy.datatypes.images:Gifti" />
Expand Down Expand Up @@ -1263,7 +1272,14 @@
<sniffer type="galaxy.datatypes.media:Mp3"/>
<sniffer type="galaxy.datatypes.media:Mp4"/>
<sniffer type="galaxy.datatypes.media:Flv"/>
<sniffer type="galaxy.datatypes.media:Ogg"/>
<sniffer type="galaxy.datatypes.media:Mpg"/>
<sniffer type="galaxy.datatypes.media:Mov"/>
<sniffer type="galaxy.datatypes.media:Avi"/>
<sniffer type="galaxy.datatypes.media:Wmv"/>
<sniffer type="galaxy.datatypes.media:Wma"/>
<sniffer type="galaxy.datatypes.media:Webm"/>
<sniffer type="galaxy.datatypes.media:Mkv"/>
<sniffer type="galaxy.datatypes.speech:TextGrid" />
<sniffer type="galaxy.datatypes.speech:BPF" />
<sniffer type="galaxy.datatypes.larch:FEFFInput" />
Expand Down
Loading
Loading