Thanks Nicola,

I didn't spot the missing slash, but planemo lint did - for anyone else copy-and-pasting:

<requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>

For anyone not yet using BioConda with Galaxy, there is also a Tool Shed entry here:

https://toolshed.g2.bx.psu.edu/view/iuc/package_galaxy_sequence_utils_1_0_1/

I am therefore adding this to my tool_dependencies.xml files:

<package name="galaxy_sequence_utils" version="1.0.1"> <repository name="package_galaxy_sequence_utils_1_0_1" owner="iuc" /> </package>

I still need to work out how best to make this available under TravisCI, given I am not currently using BioConda for the dependencies.

@IUC: Should this also be released on PyPI for easy install via pip?

Peter

On Tue, Jan 31, 2017 at 11:15 AM, Nicola Soranzo nsoranzo@tiscali.it wrote:

Hi Peter, adding

<requirement type="package" version="1.0.1">galaxy_sequence_utils<requirement>

to each of these tools should solve the problem, there is a Bioconda package which provides the Python library:

https://anaconda.org/bioconda/galaxy_sequence_utils

Cheers, Nicola

On 31/01/17 10:39, Peter Cock wrote:

...

Hi all,

A few of my tools have for a long time used Galaxy's own parsing functionality in order to avoid an external dependency. Lately this has stopped working on my TravisCI testing with planemo using the Galaxy dev branch (the stable master branch is fine): e.g.

https://travis-ci.org/peterjc/pico_galaxy/builds/196655736

The tools fail with things like:

| from galaxy_utils.sequence.fasta import fastaReader, fastaWriter | ImportError: No module named galaxy_utils.sequence.fasta

or:

| from galaxy_utils.sequence.fastq import fastqReader | ImportError: No module named galaxy_utils.sequence.fastq

Is this a temporary regression in Galaxy, or a deliberate change? Do the tools need to do something to explicit have access to the Galaxy Python library, or are they now considered private? If so, I can update these tools to use an explicit dependency for parsing FASTA and FASTQ (e.g. Biopython).

Thanks,

Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

It would also be nice to have gops in Conda, either Bioconda or iuc channel.

Cheers, Nicola

On 31/01/17 15:01, Martin Čech wrote:

Hi folks,

the two of the Galaxy-born libraries have sources at our GitHub:

https://github.com/galaxyproject/gops https://github.com/galaxyproject/sequence_utils

Any improvements or PyPI-readiness work are welcome.

Best, Martin

On Tue, Jan 31, 2017 at 7:08 AM Peter Cock <p.j.a.cock@googlemail.com mailto:p.j.a.cock@googlemail.com> wrote:

Thanks Nicola,

I didn't spot the missing slash, but planemo lint did - for anyone
else copy-and-pasting:

<requirement type="package"
version="1.0.1">galaxy_sequence_utils</requirement>

For anyone not yet using BioConda with Galaxy, there is also a Tool
Shed entry here:

https://toolshed.g2.bx.psu.edu/view/iuc/package_galaxy_sequence_utils_1_0_1/

I am therefore adding this to my tool_dependencies.xml files:

    <package name="galaxy_sequence_utils" version="1.0.1">
        <repository name="package_galaxy_sequence_utils_1_0_1"
owner="iuc" />
    </package>

I still need to work out how best to make this available under
TravisCI,
given I am not currently using BioConda for the dependencies.

@IUC: Should this also be released on PyPI for easy install via pip?

Peter


On Tue, Jan 31, 2017 at 11:15 AM, Nicola Soranzo
<nsoranzo@tiscali.it <mailto:nsoranzo@tiscali.it>> wrote:
> Hi Peter,
> adding
>
> <requirement type="package"
> version="1.0.1">galaxy_sequence_utils<requirement>
>
> to each of these tools should solve the problem, there is a
Bioconda package
> which provides the Python library:
>
> https://anaconda.org/bioconda/galaxy_sequence_utils
>
> Cheers,
> Nicola
>
>
> On 31/01/17 10:39, Peter Cock wrote:
>>
>> Hi all,
>>
>> A few of my tools have for a long time used Galaxy's own parsing
>> functionality in order to avoid an external dependency. Lately
>> this has stopped working on my TravisCI testing with planemo
>> using the Galaxy dev branch (the stable master branch is fine):
>> e.g.
>>
>> https://travis-ci.org/peterjc/pico_galaxy/builds/196655736
>>
>> The tools fail with things like:
>>
>> |  from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
>> |  ImportError: No module named galaxy_utils.sequence.fasta
>>
>>
>> or:
>>
>> |  from galaxy_utils.sequence.fastq import fastqReader
>> |  ImportError: No module named galaxy_utils.sequence.fastq
>>
>> Is this a temporary regression in Galaxy, or a deliberate change?
>> Do the tools need to do something to explicit have access to the
>> Galaxy Python library, or are they now considered private?
>> If so, I can update these tools to use an explicit dependency
>> for parsing FASTA and FASTQ (e.g. Biopython).
>>
>> Thanks,
>>
>> Peter
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
>
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/

Thanks John - that could explain what's going wrong and offers another approach to fixing my TravisCI testing - setting:

preserve_python_environment = legacy_and_local

or:

preserve_python_environment = always

(Despite several attempts I didn't hit on a nice way to get the galaxy_sequence_utils installed nicely via a "manual install", one day I will switch my TravisCI testing to use BioConda)

I am hoping to get my TravisCI builds passing again today...

Peter

On Tue, Jan 31, 2017 at 5:27 PM, John Chilton jmchilton@gmail.com wrote:

So the PR that broke your tools is probably here https://github.com/galaxyproject/galaxy/pull/3364/files. That pull request removed Galaxy from the Python path of Galaxy tools - this gives tools a much cleaner environment and prevents certain conflicts between Conda and Galaxy.

As part of that PR, there is a list of Galaxy tools in lib/galaxy/tools/__init__.py that still get setup with Galaxy's Python environment. This includes many random devteam and even an IUC tool - I've added something to the list even though one ancient version of tool shed tool required it years ago and it has since been updated. I would open a PR to add the tool id of any of your tools that have been published to the tool shed and require these tools to this list. You can target it against 17.01 ideally and then we can merge that into dev.

This behavior can be reverted - there is a config option that is documented pretty well in the PR but I missed named it in the sample (fixing it with https://github.com/galaxyproject/galaxy/pull/3521/files).

Hopefully this helps and thanks for the bug report!

-John

On Tue, Jan 31, 2017 at 7:08 AM Peter Cock p.j.a.cock@googlemail.com wrote:

...

Thanks Nicola,

I didn't spot the missing slash, but planemo lint did - for anyone else copy-and-pasting:

<requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>

For anyone not yet using BioConda with Galaxy, there is also a Tool Shed entry here:

https://toolshed.g2.bx.psu.edu/view/iuc/package_galaxy_sequence_utils_1_0_1/

I am therefore adding this to my tool_dependencies.xml files:

<package name="galaxy_sequence_utils" version="1.0.1">
    <repository name="package_galaxy_sequence_utils_1_0_1" owner="iuc"

/> </package>

I still need to work out how best to make this available under TravisCI, given I am not currently using BioConda for the dependencies.

@IUC: Should this also be released on PyPI for easy install via pip?

Peter

On Tue, Jan 31, 2017 at 11:15 AM, Nicola Soranzo nsoranzo@tiscali.it wrote:

...

Hi Peter, adding

<requirement type="package" version="1.0.1">galaxy_sequence_utils<requirement>

to each of these tools should solve the problem, there is a Bioconda package which provides the Python library:

https://anaconda.org/bioconda/galaxy_sequence_utils

Cheers, Nicola

On 31/01/17 10:39, Peter Cock wrote:

...

Hi all,

A few of my tools have for a long time used Galaxy's own parsing functionality in order to avoid an external dependency. Lately this has stopped working on my TravisCI testing with planemo using the Galaxy dev branch (the stable master branch is fine): e.g.

https://travis-ci.org/peterjc/pico_galaxy/builds/196655736

The tools fail with things like:

| from galaxy_utils.sequence.fasta import fastaReader, fastaWriter | ImportError: No module named galaxy_utils.sequence.fasta

or:

| from galaxy_utils.sequence.fastq import fastqReader | ImportError: No module named galaxy_utils.sequence.fastq

Is this a temporary regression in Galaxy, or a deliberate change? Do the tools need to do something to explicit have access to the Galaxy Python library, or are they now considered private? If so, I can update these tools to use an explicit dependency for parsing FASTA and FASTQ (e.g. Biopython).

Thanks,

Peter

To recap, in the next release of Galaxy, there will not be a copy of the sequence parsing code like lib/galaxy_utils/sequence/fastq.py - see this pull request: https://github.com/galaxyproject/galaxy/pull/3551

Both Galaxy itself, and any tools needing it, will depend on the now separately packaged galaxy_sequence_utils library, source code now here:

https://github.com/galaxyproject/sequence_utils

The original version of this is available on the Tool Shed:

https://toolshed.g2.bx.psu.edu

The library is now available on PyPI too:

https://pypi.python.org/pypi/galaxy_sequence_utils/

This code has been updated and now does "import six" as part of work to make sure it can be used on Python 2 and Python 3, and it includes support for compressed FASTQ files.

My TravisCI tool tests are passing again using both Galaxy's stable and dev branches.

Peter

On Wed, Feb 1, 2017 at 11:20 AM, Peter Cock p.j.a.cock@googlemail.com wrote:

This went smoother today, and has served to refresh some of the details of how the Galaxy's venv etc all work.

In my TravisCI setup for tool testing I currently "manually" install the tool dependencies, and thus am using pip with the same URL as the Tool Shed package:

pip install http://depot.galaxyproject.org/package/source/galaxy_sequence_utils/galaxy_s...

Commit:

https://github.com/peterjc/pico_galaxy/commit/c9b77b49281974988c790a54f05c4d...

The TravisCI build is still failing, but on an unrelated change on the Galaxy dev branch.

Peter