mvdbeek
9f8c29520d
Use virtualenv when conda is on PATH
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This uses our proper pinned requirements and is sginificantly easier
to set up and maintain.
2018-11-07 14:20:05 +01:00
Marius van den Beek
c1e4b0111a
Merge pull request #6911 from jmchilton/workflow_mapping_refactor
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Refactor collection mapping workflows toward independence from tools.
2018-11-05 14:04:09 +01:00
Marius van den Beek
a3f213e3c5
Merge pull request #6962 from bernt-matthias/topic/rma
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add RMA6 data type (MEGAN6 read-match archive)
2018-11-05 13:04:37 +01:00
M Bernt
562b10b7ef
rma: renamed test data to rma6
2018-11-05 09:26:33 +01:00
Marius van den Beek
0ede377925
Merge pull request #6957 from bernt-matthias/topic/empty-data-table
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Topic/empty data table
2018-11-04 22:13:12 +01:00
M Bernt
ee0038a01f
rma: extension rma6 for consistency
2018-11-02 17:25:05 +01:00
Nicola Soranzo
d6af6b7bd1
Merge branch 'release_18.09' into dev
2018-11-02 15:06:08 +00:00
Nicola Soranzo
357e2f39c7
Merge branch 'release_18.05' into release_18.09
2018-11-02 14:57:30 +00:00
Martin Cech
6da5157181
Merge pull request #6963 from nsoranzo/release_18.05_allow_rdata.sce_upload
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[18.05] Allow upload for ``rdata.sce`` format
2018-11-02 09:33:45 -04:00
Nicola Soranzo
6b5f0a2ad1
Allow upload for `rdata.sce` format
2018-11-02 13:18:15 +00:00
M Bernt
09de6fe496
rma: fix test
2018-11-02 09:44:26 +01:00
M Bernt
dcae06624a
rma: RMA->RMA6
2018-11-01 23:57:34 +01:00
M Bernt
0beac8fdf4
rma: add RMA6 data type (MEGAN6 read-match archive)
2018-11-01 23:46:41 +01:00
M Bernt
13a4238510
removed debug output
2018-11-01 19:10:02 +01:00
M Bernt
cc8e1c211e
fix empty loc file bug
2018-11-01 19:06:46 +01:00
mvdbeek
30aaa296dd
Fix sniffing of readname sorted BAM files
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This fixes https://github.com/galaxyproject/galaxy/issues/6949 .
The problem is that `super` would fall back to the BamInputSorted
sniffer, which prevents sniffing. Includes a test file for the new
datatype upload testing framework.
2018-11-01 12:00:38 -04:00
John Chilton
f035d642ce
Merge pull request #6844 from jmchilton/compressed_types_and_extra_files
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Infrastructure/API Support for Composite Uploads/Downloads
2018-11-01 10:57:09 -04:00
John Chilton
c312c1014d
Merge pull request #6937 from natefoo/shed-tools-relocate
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Default shed tool installation to database/shed_tools
2018-11-01 10:22:05 -04:00
Dannon
3108bd3b37
Merge pull request #6910 from guerler/toolshed_selection
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Fix style for legacy toolshed selection page
2018-11-01 08:57:24 -04:00
Martin Cech
3f7425ad93
Merge pull request #6948 from guerler/add_overflow_auto
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Use recently introduced overflow utility instead of overwriting card defaults
2018-10-31 16:21:15 -04:00
guerler
20f3c04a42
Use existing overflow utility instead of overwriting card defaults
2018-10-31 15:34:23 -04:00
Martin Cech
31905f1402
Merge pull request #6917 from dannon/unified_webpack4
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Unified webpack4
2018-10-31 14:52:32 -04:00
John Chilton
f40bb68141
Merge pull request #6950 from mvdbeek/qname_sorted_sniffer
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Fix sniffing of readname sorted BAM files
2018-10-31 10:40:10 -04:00
mvdbeek
c78f704c23
Add two test files that exercise json and txt sniffing
2018-10-31 10:03:50 +01:00
mvdbeek
ddeef3fbc2
Fix sniffing of readname sorted BAM files
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This fixes https://github.com/galaxyproject/galaxy/issues/6949 .
The problem is that `super` would fall back to the BamInputSorted
sniffer, which prevents sniffing. Includes a test file for the new
datatype upload testing framework.
2018-10-31 09:59:41 +01:00
Nicola Soranzo
b47efd4ade
Merge branch 'release_18.09' into dev
2018-10-31 09:38:34 +01:00
Dannon Baker
4d5285b659
Another image link for admin_toolshed stuff.
2018-10-30 18:44:45 -04:00
Dannon Baker
dbdce6d37b
Stage two more images after inclusion in scripts. We'll inevitably find more of these, and they should all be removed, but this gives us a way to transition as things are rewritten.
2018-10-30 17:58:28 -04:00
Dannon Baker
7dbc81ca82
Add images to default static-safe location
2018-10-30 17:41:14 -04:00
John Chilton
4c7ba6f0fe
Merge pull request #6946 from mvdbeek/bam_index_for_coordinate_sorted_only
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[18.09] Make Bam index only available for coordinate sorted bam files
2018-10-30 17:29:57 -04:00
guerler
2bf5b9b84e
Fix style for legacy toolshed selection page
2018-10-30 14:25:08 -04:00
John Chilton
17efac853a
Merge pull request #6943 from shiltemann/collection-strip-urlprefix
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Collection builder: add option to strip url prefix from pair names
2018-10-30 13:21:56 -04:00
mvdbeek
49d9409f00
Bam index is only available for coordinate sorted bam files
2018-10-30 18:09:37 +01:00
Dannon Baker
51273658fb
Merge remote-tracking branch 'upstream/dev' into unified_webpack4
2018-10-30 11:06:24 -04:00
Dannon Baker
46f24df8e1
For simplicity, just symlink viz images for now
2018-10-30 11:03:25 -04:00
Dannon Baker
b27b3fe2af
Move test files for upstream merge (case sensitivity in git)
2018-10-30 11:00:12 -04:00
Saskia Hiltemann
41d60f5761
always strip url prefix
2018-10-30 14:24:31 +01:00
John Chilton
9713556b16
Merge pull request #6869 from mvdbeek/datatype_upload_integration_test
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Datatype upload integration test and fixes
2018-10-30 09:22:12 -04:00
Saskia Hiltemann
a1b7105b38
add option to strip url prefix from pair names
2018-10-30 13:21:59 +01:00
Marius van den Beek
1482cacee5
Merge pull request #6886 from ilveroluca/fix/k8s_error_handling
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Improve k8s job error handling
2018-10-30 12:01:18 +01:00
Marius van den Beek
0de9c738cf
Merge pull request #6833 from martenson/tinies
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adjust the panel resize cursor, update docs link
2018-10-30 10:40:34 +01:00
mvdbeek
16962ad6a1
Add newline to lib/galaxy/datatypes/test/5e5z.pqr
2018-10-30 10:32:19 +01:00
mvdbeek
ba5d76eb93
Avoid exception if no match
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This fixes the sniffing unit test, the datatype framework would just
continue anyway.
2018-10-30 09:27:26 +01:00
mvdbeek
ecc02bb659
Fix UploadProblemException
2018-10-30 09:27:26 +01:00
mvdbeek
0fae117e67
Use raw strings in regex and allow lowercase fastq sequences
2018-10-30 09:27:26 +01:00
mvdbeek
c50a0fccac
Don't sniff simple json types
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These should instead be text.
2018-10-30 09:27:26 +01:00
mvdbeek
1a407429ba
Tighten up mothur and phylip sniffers
2018-10-30 09:27:26 +01:00
mvdbeek
738bde0127
Fix check_html on python 3
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We can open the file in binary mode and then use unicodify on the lines,
as we have to do that anyway if `chunks` is provided.
Also adds the unicode flag to re.compile.
2018-10-30 09:27:26 +01:00
mvdbeek
d168042b36
Fix newline conversion on python 3 if no encoding is set
2018-10-30 09:27:25 +01:00
mvdbeek
09601ad4ef
Skip newlines/space2tab conversion for binary datatypes that fail is_binary check
2018-10-30 09:27:25 +01:00
mvdbeek