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  • Jan 31 2019 17:58
    jorgemachucav starred galaxyproject/tools-iuc
  • Jan 31 2019 17:45
    bebatut opened #2270
  • Jan 31 2019 16:18
    cpreviti synchronize #2267
  • Jan 31 2019 14:15
    cpreviti synchronize #2267
  • Jan 31 2019 12:42
    bernt-matthias review_requested #2269
  • Jan 31 2019 12:42
    bernt-matthias edited #2269
  • Jan 31 2019 12:41
    bernt-matthias edited #2269
  • Jan 31 2019 12:40
    bernt-matthias synchronize #2269
  • Jan 31 2019 12:13
    cpreviti commented #2267
  • Jan 31 2019 12:07
    nsoranzo commented #2267
  • Jan 31 2019 12:01
    cpreviti synchronize #2267
  • Jan 31 2019 11:21
    cpreviti synchronize #2267
  • Jan 31 2019 09:47
    cpreviti synchronize #2267
  • Jan 31 2019 09:27
    cpreviti synchronize #2267
  • Jan 30 2019 20:38
    bernt-matthias commented #2131
  • Jan 30 2019 20:19
    hepcat72 commented #2239
  • Jan 30 2019 19:50
    lparsons commented #2239
  • Jan 30 2019 18:36
    bgruening commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2267
Robert Leach
@hepcat72
Is there a way to test a tool with "whitelisted" status in planemo?
Robert Leach
@hepcat72
I see it in the admin GUI. Is there a yaml for planemo for having it automatically whitelisted during planemo serve?
Robert Leach
@hepcat72
Whitelisting worked to clean out the css text at the top of each page and worked to decorate the text, however it appears that the embedded javascript does not work and appears to be stripped out of the page source. Is this another level of whitelisting or is javascript in html content not supported?
Dannon
@dannon
Sorry, just saw this. I'm not sure about planemo having a config override for it. And, yes, stripping untrusted code from the dataset is exactly what the sanitization does. Once whitelisted, the tool is trusted, and you can put anything you want in there.
You'd just need a way to swap sanitize_all_html to False in the configuration, but I'm not familiar with how planemo manages that.
(for easy testing with the sanitization completely disabled)
Robert Leach
@hepcat72
Thanks
Dan Fornika
@dfornika
Could someone please merge this minor update to the new bracken tool? It just modifies the way that the tool and wrapper versions are managed. galaxyproject/tools-iuc#2646
Björn Grüning
@bgruening
done
Dan Fornika
@dfornika
Thanks!
Dan Fornika
@dfornika
Hmm... The bracken version is still reported as @VERSION@+galaxy0 on the toolshed: https://toolshed.g2.bx.psu.edu/repository?repository_id=0357fb68688c419f&changeset_revision=0b967e0ceb18
Ah, I see the problem. I'll submit a fix.
Dan Fornika
@dfornika
Sorry for not catching it on the last PR. galaxyproject/tools-iuc#2650
Martin Cech
@martenson
Where is this pandas coming from? https://github.com/galaxyproject/tools-iuc/blob/master/tools/anndata/inspect.xml#L14
pvanheus
@pvanheus
@martenson from the dependencies of anndata: https://github.com/conda-forge/loompy-feedstock/blob/master/recipe/meta.yaml
Alex Ostrovsky
@astrovsky01
Alongside @martenson's question, did the way python imports work in tools change recently?
pvanheus
@pvanheus
sorry I meant loompy
change, how?
(but anndata also has a pandas dependency)
Alex Ostrovsky
@astrovsky01
I've been working on an update to this to be able to interconvert with loom files, and my script used to work, but after making some small edits, I can no longer import loompy or anndata in a python script in the tool
pvanheus
@pvanheus
despite them being in the requirements? that should not be happening
can you point me at your source?
Alex Ostrovsky
@astrovsky01
galaxyproject/tools-iuc#2420
Reverting to previous version and running the script, I get "no module named x" errors every time
Alex Ostrovsky
@astrovsky01
and @pvanheus, I'm glad to know I'm not crazy here, because it definitely worked before
Jennifer Hillman-Jackson
@jennaj
Anyone know how to fix this? Conda problem? Are using a docker galaxy and an IUC tools doesn't seem to be installed correctly. https://help.galaxyproject.org/t/snpeff-iuc-error-using-different-tools-from-package/2301
pvanheus
@pvanheus
@jennaj is the user sure that the dependency installed right?
pvanheus
@pvanheus
@bgruening I can see your point about trying to stem the explosion in the number of tools - the tool panel is getting massive (and searching has some odd jitter behaviour on poor connections)
Bérénice Batut
@bebatut
@astrovsky01 I got similar error to you. did you change sth recently on your conda? do you have conda base environment activated by default? if yes, you need to deactivate it before starting planemo (if using planemo insidi pipenv)
Marius van den Beek
@mvdbeek
@astrovsky01 this is your error:
|  adata = ad.read('/tmp/tmpGPbnmI/files/b/4/6/dataset_b4647644-f037-43be-a455-51f1dce1e07b.dat')
|  ^
|  IndentationError: unexpected indent
I don’t think anything has changed wrt how Galaxy resolves its dependencies
but Conda packages may change over time
roselucia
@roselucia
@jennaj and @pvanheus
I installed it using the default settings. The dependency was marked with a green check mark. So I guess it was installed right?
Thanks for you help!
roselucia
@roselucia
@jennaj and @pvanheus
Bildschirmfoto 2019-10-21 um 11.57.12.png

@jennaj and @pvanheus

Bildschirmfoto 2019-10-21 um 11.57.24.png

@jennaj and @pvanheus
Bildschirmfoto 2019-10-21 um 11.57.33.png
roselucia
@roselucia
@jennaj and @pvanheus
My server was updated and I installed snpeff and snpsift on the galaxy docker again. For some reason they are working now, which is perfect.
Hi, In order to annotated gnomAD frequencies with snpsift annotate, I loaded the according vcf from gnomad on my galaxy docker via URL (https://storage.googleapis.com/gnomad-public/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.17.vcf.bgz), changed the datatype into .vcf (using the pencil icon). However I get this error message when using snpsift annotate: "Unable to finish job"Galaxy | Galaxy Docker Build |.pdf
M Bernt
@bernt-matthias
@roselucia maybe check the stdout and stderr for indications of the problem.
Alex Ostrovsky
@astrovsky01
@mvdbeek this error came after fixing the tab error (which derived from the interactions between cheetah and python).
@bebatut How do I go about deactivating that? I don't think I changed anything, but I can give it a try?
Marius van den Beek
@mvdbeek
so what’s the error you’re seeing now ?
Alex Ostrovsky
@astrovsky01
ImportError: no module named anndata (Same for loompy if it comes first)
Marius van den Beek
@mvdbeek
can you show us the log for the dependency resolution ?
Alex Ostrovsky
@astrovsky01

```## Package Plan ##

environment location: /var/folders/18/6gsthhcj4jx85mn2z81pm9cm0000gn/T/conda_exec_home_i0VZ2u/.conda/envs/__anndata@_uv_

added / updated specs:

- anndata

The following NEW packages will be INSTALLED:

anndata conda-forge/noarch::anndata-0.6.22.post1-py_1
bzip2 conda-forge/osx-64::bzip2-1.0.8-h01d97ff_1
ca-certificates conda-forge/osx-64::ca-certificates-2019.9.11-hecc5488_0
certifi conda-forge/osx-64::certifi-2019.9.11-py37_0
h5py conda-forge/osx-64::h5py-2.10.0-nompi_py37h6248fd5_100
hdf5 conda-forge/osx-64::hdf5-1.10.5-nompi_h15a436c_1103
libblas conda-forge/osx-64::libblas-3.8.0-14_openblas
libcblas conda-forge/osx-64::libcblas-3.8.0-14_openblas
libcxx conda-forge/osx-64::libcxx-9.0.0-0
libcxxabi conda-forge/osx-64::libcxxabi-9.0.0-0
libffi conda-forge/osx-64::libffi-3.2.1-h6de7cb9_1006
libgfortran conda-forge/osx-64::libgfortran-4.0.0-2
liblapack conda-forge/osx-64::liblapack-3.8.0-14_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.7-h4bb4525_2
llvm-openmp conda-forge/osx-64::llvm-openmp-9.0.0-h40edb58_0
natsort conda-forge/noarch::natsort-6.0.0-py_0
ncurses conda-forge/osx-64::ncurses-6.1-h0a44026_1002
numpy conda-forge/osx-64::numpy-1.17.2-py37h6b0580a_0
openssl conda-forge/osx-64::openssl-1.1.1c-h01d97ff_0
pandas conda-forge/osx-64::pandas-0.25.1-py37h86efe34_0
pip conda-forge/osx-64::pip-19.3.1-py37_0
python conda-forge/osx-64::python-3.7.3-h93065d6_1
python-dateutil conda-forge/noarch::python-dateutil-2.8.0-py_0
pytz conda-forge/noarch::pytz-2019.3-py_0
readline conda-forge/osx-64::readline-8.0-hcfe32e1_0
scipy conda-forge/osx-64::scipy-1.3.1-py37h7e0e109_2
setuptools conda-forge/osx-64::setuptools-41.4.0-py37_0
six conda-forge/osx-64::six-1.12.0-py37_1000
sqlite conda-forge/osx-64::sqlite-3.30.1-h93121df_0
tk conda-forge/osx-64::tk-8.6.9-h2573ce8_1003
wheel conda-forge/osx-64::wheel-0.33.6-py37_0
xz conda-forge/osx-64::xz-5.2.4-h1de35cc_1001
zlib conda-forge/osx-64::zlib-1.2.11-h0b31af3_1006

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata: ...working... done
Solving environment: ...working... done

Package Plan

environment location: /var/folders/18/6gsthhcj4jx85mn2z81pm9cm0000gn/T/conda_exec_home_69x_IQ/.conda/envs/__loompy@_uv_

added / updated specs:

- loompy

The following NEW packages will be INSTALLED:

ca-certificates conda-forge/osx-64::ca-certificates-2019.9.11-hecc5488_0
certifi conda-forge/osx-64::certifi-2019.6.16-py36_1
h5py conda-forge/osx-64::h5py-2.10.0-nompi_py36h6248fd5_100
hdf5 conda-forge/osx-64::hdf5-1.10.5-nompi_h15a436c_1103
libblas conda-forge/osx-64::libblas-3.8.0-14_openblas
libcblas conda-forge/osx-64::libcblas-3.8.0-14_openblas
libcxx conda-forge/osx-64::libcxx-9.0.0-0
libcxxabi conda-forge/osx-64::libcxxabi-9.0.0-0
libffi conda-forge/osx-64::libffi-3.2.1-h6de7cb9_1006
libgfortran conda-forge/osx-64::libgfortran-4.0.0-2
liblapack conda-forge/osx-64::liblapack-3.8.0-14_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.7-h4bb4525_2
llvm-openmp conda-forge/osx-64::llvm-openmp-9.0.0-h40edb58_0
loompy conda-forge/noarch::loompy-2.0.17-py_0
ncurses conda-forge/osx-64::ncurses-6.1-h0a44026_1002
numpy conda-forge/osx-64::numpy-1.17.2-py36h6b0580a_0
openssl conda-forge/osx-64::openssl-1.1.1c-h01d97ff_0
pandas conda-forge/osx-64::pandas-0.25.1-py36h86efe34_0
```

```pip conda-forge/osx-64::pip-19.3.1-py36_0
python conda-forge/osx-64::python-3.6.7-h94afb7f_1005
python-dateutil conda-forge/noarch::python-dateutil-2.8.0-py_0
pytz conda-forge/noarch::pytz-2019.3-py_0
readline conda-forge/osx-64::readline-8.0-hcfe32e1_0
scipy conda-forge/osx-64::scipy-1.3.1-py36h7e0e109_2
setuptools conda-forge/osx-64::setuptools-41.4.0-py36_0
six conda-forge/osx-64::six-1.12.0-py36_1000
sqlite conda-forge/osx-64::sqlite-3.30.1-h93121df_0
tk conda-forge/osx-64::tk-8.6.9-h2573ce8_1003
typing conda-forge/osx-64::typing-3.6.4-py36_0
wheel conda-forge/osx-64::wheel-0.33.6-py36_0
xz conda-forge/osx-64::xz-5.2.4-h1de35cc_1001
zlib conda-forge/osx-64::zlib-1.2.11-h0b31af3_1006

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata: ...working... done
Solving environment: ...working... done

Package Plan

environment location: /var/folders/18/6gsthhcj4jx85mn2z81pm9cm0000gn/T/conda_exec_homeIYBva/.conda/envs/__h5py@_uv_

added / updated specs:

- h5py

The following NEW packages will be INSTALLED:

bzip2 conda-forge/osx-64::bzip2-1.0.8-h01d97ff_1
ca-certificates conda-forge/osx-64::ca-certificates-2019.9.11-hecc5488_0
certifi conda-forge/osx-64::certifi-2019.9.11-py37_0
h5py conda-forge/osx-64::h5py-2.10.0-nompi_py37h6248fd5_100
hdf5 conda-forge/osx-64::hdf5-1.10.5-nompi_h15a436c_1103
libblas conda-forge/osx-64::libblas-3.8.0-14_openblas
libcblas conda-forge/osx-64::libcblas-3.8.0-14_openblas
libcxx conda-forge/osx-64::libcxx-9.0.0-0
libcxxabi conda-forge/osx-64::libcxxabi-9.0.0-0
libffi conda-forge/osx-64::libffi-3.2.1-h6de7cb9_1006
libgfortran conda-forge/osx-64::libgfortran-4.0.0-2
liblapack conda-forge/osx-64::liblapack-3.8.0-14_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.7-h4bb4525_2
llvm-openmp conda-forge/osx-64::llvm-openmp-9.0.0-h40edb58_0
ncurses conda-forge/osx-64::ncurses-6.1-h0a44026_1002
numpy conda-forge/osx-64::numpy-1.17.2-py37h6b0580a_0
openssl conda-forge/osx-64::openssl-1.1.1c-h01d97ff_0
pip conda-forge/osx-64::pip-19.3.1-py37_0
python conda-forge/osx-64::python-3.7.3-h93065d6_1
readline conda-forge/osx-64::readline-8.0-hcfe32e1_0
setuptools conda-forge/osx-64::setuptools-41.4.0-py37_0
six conda-forge/osx-64::six-1.12.0-py37_1000
sqlite conda-forge/osx-64::sqlite-3.30.1-h93121df_0
tk conda-forge/osx-64::tk-8.6.9-h2573ce8_1003
wheel conda-forge/osx-64::wheel-0.33.6-py37_0
xz conda-forge/osx-64::xz-5.2.4-h1de35cc_1001
zlib conda-forge/osx-64::zlib-1.2.11-h0b31af3_1006

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done```

Nicola Soranzo
@nsoranzo
It's not created a mulled environment.
Marius van den Beek
@mvdbeek
anndata and loompy are both being installed as unversioned
what’s your planemo version ?
and how do you test ?
Alex Ostrovsky
@astrovsky01
0.62.0.dev0, and I run planemo test from my local galaxy root dir. @nsoranzo, the log says earlier that it did create a mulled env.
Marius van den Beek
@mvdbeek
can you give us the commandline, and does it work if you just planemo test tool.xml ?