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Add JBrowse2 #6021

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0eabcdc
Jbrowse2 tool, still wip
abretaud Sep 30, 2021
71ff77a
fix
abretaud Sep 30, 2021
9028aba
update to 1.6.4
abretaud Feb 4, 2022
cbac152
remove the standalone option, not very useful for jbrowse2
abretaud Feb 4, 2022
0fefb89
genetic code not available yet
abretaud Feb 4, 2022
96a2bc0
sparql
abretaud Feb 11, 2022
2df4afb
sparql
abretaud Feb 15, 2022
d04b003
add synteny track
abretaud Feb 15, 2022
04a72bb
add cram
abretaud Feb 16, 2022
edd06cf
add vcf_bgzip
abretaud Feb 16, 2022
8e17b46
auto conversion does the job
abretaud Feb 16, 2022
78cd9e1
add hic
abretaud Feb 16, 2022
91e781d
add default session + general options
abretaud Feb 18, 2022
b79cae1
update citation
abretaud Feb 21, 2022
80f1c91
Some progress to preconfigure a default session with default tracks a…
abretaud Feb 22, 2022
b4c7027
Run code through black
hexylena Jan 26, 2024
e7d61a5
Import Ross's changes
fubar2 Jan 26, 2024
0f0ca09
Everything required for assemblies.
hexylena Jan 26, 2024
9f30129
The python version is mostly whitespace
hexylena Jan 26, 2024
7a5ea4a
working default behaviour
hexylena Jan 26, 2024
fabace7
optional cwd
hexylena Jan 26, 2024
7b674da
Handle data relatively
hexylena Jan 26, 2024
2095650
working multi-assembly synteny
hexylena Jan 29, 2024
fead3a5
cleanup test data dir
hexylena Jan 29, 2024
b0e1a67
fix linting
hexylena Feb 15, 2024
55823fd
new release + fix version
abretaud Feb 23, 2024
7b5bc90
switch back to install from bioconda/biocontainer
abretaud Feb 27, 2024
367614a
rework default view mechanism
abretaud Mar 6, 2024
ddb61d3
fix abs/rel path problems + add cram test
abretaud Mar 6, 2024
8b49580
fix id collisions
abretaud Mar 12, 2024
a61f066
Support track display choice
abretaud Mar 12, 2024
d07d27d
fix bw
abretaud Mar 12, 2024
8f250f6
add back tests + udpate todo
abretaud Mar 7, 2023
b1e0201
add jbrowse2 - sorta works a bit - bed and reference only
fubar2 Dec 24, 2023
49c627a
got some things working...bed, gff, bw, ..
fubar2 Dec 24, 2023
998bb7d
updated bcbio-gff ;0 to 0.7.0 - bcbiogff stopped at 0.6.6
fubar2 Dec 25, 2023
970ae5a
more or less working - doesn't open default session although it's in …
fubar2 Dec 26, 2023
bc8def9
odd. failing planemo test but runs fine.
fubar2 Dec 26, 2023
2c8bdc6
profile 22.05 breaks with boolean instead of select parameters for co…
fubar2 Dec 27, 2023
9c5bb11
passes planemo tests and lint now :)
fubar2 Dec 27, 2023
0baeadd
minor cleanup
fubar2 Dec 27, 2023
1a09de3
fixed shed.yml :(
fubar2 Dec 27, 2023
8427e7d
get rid of some cruft.
fubar2 Dec 27, 2023
57cf121
and more cruft
fubar2 Dec 27, 2023
86db100
Must remove jbrowse-from-dir.xml because it will always fail linting …
fubar2 Dec 27, 2023
7104451
shuffling lines to appease the robot pedants.
fubar2 Dec 27, 2023
71a3f8a
robot pedants will always win.
fubar2 Dec 27, 2023
7a1b33d
thought this was done
fubar2 Dec 27, 2023
a543771
whoopsie - "fixed" the wrong shed.yml :(
fubar2 Dec 27, 2023
1717003
evil twins
fubar2 Dec 27, 2023
3c8776e
fix readme.rst - didn't see it :(
fubar2 Dec 27, 2023
3608161
fix cp
fubar2 Dec 27, 2023
1c08e2c
cannot get sample vcf to work - header problem reported - tweaking ad…
fubar2 Dec 27, 2023
792484e
flake8 hanging indents fixed...
fubar2 Dec 27, 2023
df6c0be
Update jbrowse2.xml
bgruening Dec 27, 2023
ea14dae
style formatting
bgruening Dec 27, 2023
70e6a03
add profile version and fix version command
bgruening Dec 27, 2023
795eed5
testing maf
fubar2 Dec 28, 2023
e9c9e28
maf now added - runs and seems to make a track of 3.maf from test-dat…
fubar2 Dec 28, 2023
43640dc
adding files to branch
fubar2 Dec 28, 2023
e16f2e6
add jbrowse2 - sorta works a bit - bed and reference only
fubar2 Dec 24, 2023
a65b57f
got some things working...bed, gff, bw, ..
fubar2 Dec 24, 2023
3221a81
updated bcbio-gff ;0 to 0.7.0 - bcbiogff stopped at 0.6.6
fubar2 Dec 25, 2023
b33889c
more or less working - doesn't open default session although it's in …
fubar2 Dec 26, 2023
561a145
odd. failing planemo test but runs fine.
fubar2 Dec 26, 2023
a46750d
profile 22.05 breaks with boolean instead of select parameters for co…
fubar2 Dec 27, 2023
67ea331
passes planemo tests and lint now :)
fubar2 Dec 27, 2023
6db2883
minor cleanup
fubar2 Dec 27, 2023
2378b80
fixed shed.yml :(
fubar2 Dec 27, 2023
35c3405
get rid of some cruft.
fubar2 Dec 27, 2023
a5f5f61
and more cruft
fubar2 Dec 27, 2023
f548b69
Must remove jbrowse-from-dir.xml because it will always fail linting …
fubar2 Dec 27, 2023
8c6d9cb
shuffling lines to appease the robot pedants.
fubar2 Dec 27, 2023
6999970
robot pedants will always win.
fubar2 Dec 27, 2023
de0cb4a
thought this was done
fubar2 Dec 27, 2023
0e17f9e
whoopsie - "fixed" the wrong shed.yml :(
fubar2 Dec 27, 2023
0974d82
evil twins
fubar2 Dec 27, 2023
47b86e9
fix readme.rst - didn't see it :(
fubar2 Dec 27, 2023
585ce51
fix cp
fubar2 Dec 27, 2023
d827b3a
cannot get sample vcf to work - header problem reported - tweaking ad…
fubar2 Dec 27, 2023
8459189
flake8 hanging indents fixed...
fubar2 Dec 27, 2023
3b127fa
Update jbrowse2.xml
bgruening Dec 27, 2023
667cdcc
style formatting
bgruening Dec 27, 2023
4195dd8
add profile version and fix version command
bgruening Dec 27, 2023
6979205
testing maf
fubar2 Dec 28, 2023
102a059
maf now added - runs and seems to make a track of 3.maf from test-dat…
fubar2 Dec 28, 2023
9339f7c
flake8 satisfied
fubar2 Dec 28, 2023
c8ceaae
maf seems to work with some test data - naming of chromosomes and ref…
fubar2 Dec 29, 2023
539076c
flakery fixed
fubar2 Dec 29, 2023
114353b
Update tools/jbrowse2/jbrowse2.xml
fubar2 Dec 29, 2023
4741c74
fixed broken test.
fubar2 Dec 29, 2023
47c588c
creating branch with hic ready to test
fubar2 Dec 30, 2023
fad0ca5
hic works!
fubar2 Jan 2, 2024
2ea3165
HiC working - the HiC file and the reference now served from a URL so…
fubar2 Jan 2, 2024
4ccd136
odd. passes planemo lint here but fails on ci
fubar2 Jan 2, 2024
ad9face
trying removing profile= from tool to see if planemo lint stops compl…
fubar2 Jan 2, 2024
651ae01
nope. not the problem. profile restored.
fubar2 Jan 2, 2024
3048d69
fixes to restore maf functionality. Now have blast, maf, bed, bam, gf…
fubar2 Jan 2, 2024
8585b32
fix flake8 complaints. Still fails - some CI planemo lint failure?
fubar2 Jan 2, 2024
21b9bf2
fixes for blastxml_to_gapped_gff3.py - works with a PR submitted to b…
fubar2 Jan 3, 2024
c80580c
remove test_data from JBrowse clone - much smaller archive now.
fubar2 Jan 3, 2024
b9aab79
fix bogus import for flake8
fubar2 Jan 3, 2024
613c6b3
add tabix for bed to see if empty seqtk telo track still causes troub…
fubar2 Jan 3, 2024
5353bb0
datatypes_conf fix
fubar2 Jan 3, 2024
7e396e1
added datatypes_conf.xml :( no wonder it didn't work
fubar2 Jan 3, 2024
b273aee
datatypes_conf.xml content is now ignored so remove.
fubar2 Jan 3, 2024
3aa5585
Changes to allow minimal to use URLs where possible and complete to i…
fubar2 Jan 4, 2024
8e502d6
big cleanup.
fubar2 Jan 5, 2024
054e0e4
odd. lint failed.
fubar2 Jan 5, 2024
ed3fffc
fix flake error and lint
fubar2 Jan 5, 2024
e30ffb7
local flake differs
fubar2 Jan 5, 2024
a4a8f61
fix odd problem with spaces in reference names - should be chosen wit…
fubar2 Jan 5, 2024
6b76b3c
fixes to deal with different directory structures in conda environmen…
fubar2 Jan 5, 2024
e14101b
passes tests in biocontainers at last.
fubar2 Jan 5, 2024
a49b4c9
incorporated most of @abretaud's #3997
fubar2 Jan 7, 2024
ee6b0e6
passes 4 tests but not with biocontainers :(
fubar2 Jan 7, 2024
f6d562c
Incorporate all the things missing from abretadeu's #3997
fubar2 Jan 7, 2024
dda7f4a
tests added for vcf and wiggle. Problem with bam - upload always dete…
fubar2 Jan 8, 2024
2f1fd9f
passing 6 tests biocontainers too.
fubar2 Jan 8, 2024
3398c39
rename back to lowercase for consistency and planemo
fubar2 Jan 8, 2024
7fe902d
update to 1.6.4
abretaud Feb 4, 2022
c735c1d
fixes after rebase
abretaud Feb 4, 2022
d00fc83
rebasing is hard
abretaud Feb 4, 2022
b3ea5c7
getting harder...
abretaud Feb 11, 2022
a3eaeab
still stuck. eeesh rebase.
abretaud Feb 15, 2022
7b781c8
still stuck. infuriating business this.
abretaud Feb 15, 2022
f5c6417
This is mad. Try removing xml and py sources of repeated merge failur…
abretaud Feb 16, 2022
e120207
about to give up
abretaud Feb 16, 2022
fe26bd8
add hic
abretaud Feb 16, 2022
641ae94
add default session + general options
abretaud Feb 18, 2022
1414917
update citation
abretaud Feb 21, 2022
f810760
Some progress to preconfigure a default session with default tracks a…
abretaud Feb 22, 2022
460326e
Final fixes after rebasing to abretaud PR for Helena
fubar2 Jan 9, 2024
1d44168
some fixes suggested by @hexylena
fubar2 Jan 9, 2024
f9e19d6
Update tools/jbrowse2/jbrowse2.xml
fubar2 Jan 9, 2024
b51363e
Update tools/jbrowse2/macros.xml
fubar2 Jan 9, 2024
29c2957
forgot to save...
fubar2 Jan 9, 2024
df7f5cd
fix renamed webserver.py causeing test failure :(
fubar2 Jan 9, 2024
413ebe2
remove noisy logging and printing of progress.
fubar2 Jan 9, 2024
35c6836
add linearpileupdisplay to solve the long loading times for bed track…
fubar2 Jan 9, 2024
9c5f8b8
add styles back
fubar2 Jan 9, 2024
2f2cf7e
expand initial view window
fubar2 Jan 9, 2024
495c76d
remove names from filenames - they can have tricks in them such as /
fubar2 Jan 10, 2024
ebb0d97
updates to current code on EU
fubar2 Mar 26, 2024
1c0bcd3
Revert "Add bio.tools for abriTAMR (#5561)"
fubar2 Mar 26, 2024
9714bd4
Revert "Revert "Add bio.tools for abriTAMR (#5561)""
fubar2 Mar 26, 2024
5da583c
Revert "updates to current code on EU"
fubar2 Mar 26, 2024
8d73153
current EU and github code for JBrowse2
fubar2 Mar 26, 2024
e993a53
Jbrowse2 tool, still wip
abretaud Sep 30, 2021
29988c2
Run code through black
hexylena Jan 26, 2024
40b0b75
Import Ross's changes
fubar2 Jan 26, 2024
be07fca
Everything required for assemblies.
hexylena Jan 26, 2024
88e01c9
The python version is mostly whitespace
hexylena Jan 26, 2024
73ed397
working default behaviour
hexylena Jan 26, 2024
ad21772
optional cwd
hexylena Jan 26, 2024
becd182
Handle data relatively
hexylena Jan 26, 2024
158ffa9
working multi-assembly synteny
hexylena Jan 29, 2024
897e079
switch back to install from bioconda/biocontainer
abretaud Feb 27, 2024
525626b
rework default view mechanism
abretaud Mar 6, 2024
1b85fc1
fix abs/rel path problems + add cram test
abretaud Mar 6, 2024
25fe825
fix id collisions
abretaud Mar 12, 2024
da7dce7
Support track display choice
abretaud Mar 12, 2024
6636bd4
fix bw
abretaud Mar 12, 2024
dc3b59b
lots of challenges from the rebase with the extra layer of repeats fo…
fubar2 Mar 26, 2024
7155f65
working with 2 assemblies in a test.
fubar2 Mar 28, 2024
1f402e0
some tests working - still need fixin'
fubar2 Mar 28, 2024
e7ec48b
tests all passing. removed one with failing menu fussery.
fubar2 Mar 28, 2024
4ee1e53
a collection, and 8 phage small samples with hg38 hic URI demonstrati…
fubar2 Mar 28, 2024
b6efb64
got collection working again...mixed up versions on dev.au - all good…
fubar2 Mar 28, 2024
e2ffa24
ensure no spaces in genome uri track names for paf
fubar2 Mar 29, 2024
6cbda57
fix collections again. Now that assemblies are written last..
fubar2 Mar 29, 2024
b8ea3f2
remove bogus % signs
fubar2 Mar 29, 2024
c3c08c8
and more % go.
fubar2 Mar 29, 2024
2b3de83
leave debug logging on and convert warn to debug
fubar2 Mar 29, 2024
98b8abb
remove old broken pl
fubar2 Mar 29, 2024
3a0af4d
add creators, fix version
bgruening Mar 29, 2024
4d2a299
tighten up the logging
bgruening Mar 30, 2024
9eee49b
remove explicit EDAM in favor of biotools annotation
bgruening Mar 30, 2024
e8d1ace
remove autgenJB2 tool, this is now integrated into the main tool
bgruening Mar 30, 2024
f284d9f
revert suite based shed file
bgruening Mar 30, 2024
a3831bc
cleanups
bgruening Mar 29, 2024
8bc6356
fixes for pafs with multiple shared references
bgruening Mar 31, 2024
c19e607
misc additions
bgruening Mar 31, 2024
8fa9fe5
add zip test
bgruening Apr 1, 2024
67d2243
Update tools/jbrowse2/autogenJB2.py
bgruening Apr 1, 2024
e4dadad
Apply suggestions from code review
bgruening Apr 1, 2024
3875b29
tweak tests
bgruening Apr 1, 2024
c8213d7
add complex test
bgruening Apr 1, 2024
17815e1
cram not pileup
bgruening Apr 1, 2024
93befea
handle default session more gracefully
bgruening May 20, 2024
b260824
handle more tracks
bgruening May 20, 2024
2123412
update readme with latest changes from Ross
bgruening May 20, 2024
fa7ec79
add EDAM and update dependencies+
bgruening May 20, 2024
ae39c5f
reformat with VSC and the GLS
bgruening May 20, 2024
1723c9d
add image linked in readme
bgruening May 20, 2024
ae2fbd7
add track_styling_vgp macro
bgruening May 20, 2024
31d9a76
simplify pafref handling
bgruening May 20, 2024
4f5f9e4
introduce index_template
bgruening May 20, 2024
2c4576c
take over changes from Ross and fix strange bug with contig handling
bgruening May 20, 2024
973101d
better handling of HiC data
bgruening May 20, 2024
4ce3224
improve BAM and CRAM handling
bgruening May 20, 2024
78e1d4b
improve PAF handling
bgruening May 20, 2024
7a5007d
merge in trackset with hash from Anthony
bgruening May 20, 2024
cc547cc
merge in more changes from the other branch
bgruening May 20, 2024
9e32e1e
remove uglyTestingHack for real
bgruening May 20, 2024
7d6bc1c
use remote (location) test data and adopt tests to include more tracks
bgruening May 20, 2024
14dc5df
add more help and creators for real
bgruening May 20, 2024
9d271ba
remove deprecated warnings
bgruening May 20, 2024
2593e59
fix Galaxy linting
bgruening May 20, 2024
4197552
remove ugly testing hack
bgruening May 20, 2024
750513a
fix SSL errors
bgruening May 20, 2024
f90dff9
final cleanup, tests are passing now again
bgruening May 20, 2024
6bb5b7a
remove unused file
bgruening May 22, 2024
0232f6f
remove unused file
bgruening May 22, 2024
5b2fd5d
update JBrowse2
bgruening May 27, 2024
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odd. lint failed.
  • Loading branch information
fubar2 authored and bgruening committed May 21, 2024
commit 054e0e462cb0b39c1926dc97fb2efd5879cac343
2 changes: 1 addition & 1 deletion tools/jbrowse2/jbrowse2.xml
Original file line number Diff line number Diff line change
@@ -405,7 +405,7 @@ Assuming you have python3 installed, running

*python3 servjb2.py*

will serve the unarchived JBrowse2 configuration, so it can be browsed by pointing a web browser to *http://localhost:8080*
will serve the unarchived JBrowse2 configuration, so it can be browsed by pointing a web browser to localhost:8080

Overview
--------