Re: [galaxy-dev] How to include local tools with Docker image of Galaxy ?

[Björn Grüning]

Hi,

sure this is possible! :)
We have some small documentation about this here:

https://github.com/bgruening/docker-galaxy-stable/#integrating-non-tool-shed-tools-into-the-container--toc

Cheers,
Bjoern

Am 01.02.2017 um 16:31 schrieb Md. Rezaul Karim:
> Dear All,
> 
> I'm a new user of Galaxy. I have been exploring the things and trying to
> use the Docker image of Galaxy. Eventually, I am planning to run the
> docker container on our local Cluster.
> 
> I was wondering if there's any way to include local tools with the
> Dockerfile. For example using the Docker image of Galaxy at
> https://github.com/bgruening/docker-galaxy-stable it shows how to
> include the tools to the Docker image of Galaxy from the Galaxy tool
> shed as follows:
> 
> RUN install-repository \
> "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name
> package_numpy_1_7" \
> "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name
> package_perl_pdf_api2_2_023" \
> 
> This command will pull the tools from the Galaxy tool shed and install
> inside the docker container. But, is there's any similar way to include
> my own local tools?
> 
> 
> 
> 
> Regards,
> _
> *Md. Rezaul Karim*, BSc, MSc
> PhD Researcher, INSIGHT Centre for Data Analytics
> National University of Ireland, Galway
> IDA Business Park, Dangan, Galway, Ireland
> Web: http://www.reza-analytics.eu/index.html
> 
> 
> 
> ___
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Re: [galaxy-dev] Request more details from Nikolaos Tur about pyBamTools & pyBamParser dependency packages message

[Jennifer Hsieh]

Thank so much!
This is exactly what I needed.
What a gem :)

Best,
Jen

On Tue, Jan 31, 2017 at 3:48 PM, Nikolaos Tur 
wrote:

> Hi,
>
> sorry for long delay answer. Solution which Peter suggested is absolutely
> right - owner of packages has to add changes.
> Because I did not have any reaction to my message but needed quick
> solution and wanted to stay in consistent with
> standard Galaxy installation procedure and neither do any fork of Daniel's
> packages and setup then local toolsched
> repository for tools or install these packages locally, I did some trick.
>
> First I installed these packages. Installation of course failed. Then I
> open them in web interface, uninstalled them,
> modified  tool_dependencies.xml files (see below) and installed them again
> from the web interface.
> Sorry if I miss something that was several months ago.
>
> shell_command was modified.
>
> ...
> 
> hg clone -r 
> ba0341816b15fff5e0a554658d6579a60e1b12b1
> https://bitbucket.org/dan/pybamtools pyBamTools
> $INSTALL_DIR/lib/python
> export 
> PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python
> && sed -i '/use_setuptools()/ s/^/#/' setup.py && sed -i '/from
> distribute_setup import use_set
> uptools/ s/^/#/' setup.py && python setup.py install --home
> $INSTALL_DIR
> 
> $INSTALL_
> DIR/lib/python
> 
> 
> ...
>
> instead of
>
> export 
> PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python
> && python setup.py install --home $INSTALL_DIR
>
> Idea I think is clear, after clone of tools, modify first setup.py files
> and then compile and install.
>
> Hope it can be useful,
> Nikolaos.
>
> On Tue, Jan 10, 2017 at 12:54 PM, Jennifer Hsieh  > wrote:
>
>> Hi Peter,
>> Thank you so much.
>> I'll see what I can figure out with these pull requests. I'm still quite
>> inexperienced with these types of files. This is probably a good
>> opportunity to learn some new code/structures.
>> If I can't manage to figure it out, I hope there's another variant caller
>> with different dependencies I can use for my project.
>>
>> Best,
>> Jen
>>
>>
>> On 9 Jan 2017 4:06 p.m., "Peter Briggs" 
>> wrote:
>>
>> Hello Jennifer
>>
>> I came across the same problem with the naive variant caller at the end
>> of last year, when trying to upgrade our local Galaxy instance.
>>
>> As you describe, the issue is actually with the two dependency packages:
>>
>> -- package_pybamparser_0_0_1
>> -- package_pybamtools_0_0_2
>>
>> I think I found the same solution as Nikolaos to the underlying problem
>> (i.e. the setup.py files in these two packages are no longer compatible
>> with the newer versions of the Python 'setuptools'), but I didn't have time
>> to follow it up then.
>>
>> I've now submitted pull requests with my attempted fixes on the Bitbucket
>> repositories which hold the source code for the dependencies (URLs below),
>> so at least you can see how I've tried to address the problem. However I
>> don't know of an easy way to apply these changes inside the Galaxy context
>> - my hope is that the tool maintainer (Daniel Blankenberg, cc'ed) will take
>> a look and update the dependencies on the toolshed.
>>
>> Not sure if this helps - maybe someone else on this list has a way to
>> apply the patches directly?
>>
>> Best wishes
>>
>> Peter
>>
>> Pull request URLs:
>>
>> -- https://bitbucket.org/dan/pybamtools/pull-requests/1/
>> -- https://bitbucket.org/dan/pybamparser/pull-requests/3/
>>
>>
>>
>> On 06/01/17 14:50, Jennifer Hsieh wrote:
>>
>>> Hi,
>>> I've installed a local instance of Galaxy (on Ubuntu 16.04, python
>>> 2.7.12) and have run in to this exact problem
>>> (posted by Nikolaos
>>> Tur https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.
>>> org/msg03955.html)
>>> while trying to add naive_variant_caller tool.
>>> Naive_variant_caller can't install because these two dependency packages
>>> can't be installed.
>>> I basically get exactly the same error message that ends with "IOError:
>>> Could not build the egg."
>>>
>>> Unfortunately I'm very new to both Galaxy and Python (Taking Coursera
>>> Galaxy course at the moment) and I don't really understand the solution
>>> Nikolaos described about modifying the setup.py to use "setuptools"
>>> instead of "distribute". I don't even know where to find setup.py...
>>>
>>> Can anyone help me with step-by-step details as to how to solve this
>>> dependency problem?
>>>
>>> Much Thanks!
>>> --
>>> Jennifer Hsieh
>>> PhD Neuroscience (student)
>>> Department of Psychiatry and Mental Health
>>> University of Cape Town
>>> Tell: +27 21 447 3157
>>> Cell: +27 74 841 4761
>>>
>>>
>>>
>>>
>>>
>>> ___
>>> 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/
>>>
>>>
>> --
>>

[galaxy-dev] How to include local tools with Docker image of Galaxy ?

[Md. Rezaul Karim]

Dear All,

I'm a new user of Galaxy. I have been exploring the things and trying to
use the Docker image of Galaxy. Eventually, I am planning to run the docker
container on our local Cluster.

I was wondering if there's any way to include local tools with the
Dockerfile. For example using the Docker image of Galaxy at
https://github.com/bgruening/docker-galaxy-stable it shows how to include
the tools to the Docker image of Galaxy from the Galaxy tool shed as
follows:

RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_numpy_1_7"
\
"--url https://toolshed.g2.bx.psu.edu/ -o iuc --name
package_perl_pdf_api2_2_023" \

This command will pull the tools from the Galaxy tool shed and install
inside the docker container. But, is there's any similar way to include my
own local tools?




Regards,
_
*Md. Rezaul Karim*, BSc, MSc
PhD Researcher, INSIGHT Centre for Data Analytics
National University of Ireland, Galway
IDA Business Park, Dangan, Galway, Ireland
Web: http://www.reza-analytics.eu/index.html

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Re: [galaxy-dev] Peter Cock

[Peter Cock]

Thank you,

Peter

On Wed, Feb 1, 2017 at 3:11 PM, Eduardo de Paiva Alves
 wrote:
> Hi Peter,
>
> I am wrapping https://rostlab.org/owiki/index.php/Tmseg which takes a
> PSSM matrix as one of the inputs so I will add the psiblast locally
> and test and let yo know how it goes.
>
> Thank you
>
> Eduardo
>
> On 01/02/2017 10:10, "Peter Cock"  wrote:
>
>
> Hi Eduardo,
>
>
> Certainly when Luobin Yang submitted the early work on the
> PSI BLAST wrapper we need the PSSM datatype to be defined,
> but as you note, that has been done:
>
> https://github.com/peterjc/galaxy_blast/commit/65252ee61fdd98e52454ff045fa069f04ec40c06
>
> According to the minimal notes I made on the issue for finishing
> the PSI BLAST wrapper, it is just help text and unit tests needed
> (which would include active user testing):
>
> https://github.com/peterjc/galaxy_blast/issues/19
>
> If you are a PSI BLAST user, it would be very helpful to have
> your input here.
>
> Right now the wrapper is on the TravisCI blacklist because
> it would fail testing. Likewise it is not included in the Tool Shed.
>
> Peter
>
> On Wed, Feb 1, 2017 at 9:47 AM, De paiva Alves, Eduardo
>  wrote:
> Peter
>
> I noticed there is now a PSSM datatype which is used by NCBI BLAST+
> makeprofiledb. Does that allow you to remove psiblast from blacklist in
> your repository?
>
>
> https://github.com/peterjc/galaxy_blast/blob/13d5b6deca0663d7f1301428574720
> b19aea1380/.tt_blacklist
>
>
> Thank you
>
> Eduardo
>
>
> On Tue, Feb 5, 2013 at 4:28 PM, Peter Cock <[hidden email]> wrote:
> Thanks Luobin,
>
> I've checked that into my development repository (on my tools branch):
> https://bitbucket.org/peterjc/galaxy-central/commits/f8f43f8494abdd228998d4
> e9fe67b0f2378494e0
>
> That will allow me to track changes etc as we work on the datatypes.
> Note I am not yet including ncbi_psiblast_wrapper.xml on the Galaxy
> Tool Shed.
>
> Regards,
>
> Peter
>
>
>
> The University of Aberdeen is a charity registered in Scotland, No SC013683.
> Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. 
> SC013683
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
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>   http://galaxyproject.org/search/mailinglists/
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[galaxy-dev] Peter Cock

[Eduardo de Paiva Alves]

Hi Peter,

I am wrapping https://rostlab.org/owiki/index.php/Tmseg which takes a
PSSM matrix as one of the inputs so I will add the psiblast locally
and test and let yo know how it goes.

Thank you

Eduardo

On 01/02/2017 10:10, "Peter Cock"  wrote:


Hi Eduardo,


Certainly when Luobin Yang submitted the early work on the
PSI BLAST wrapper we need the PSSM datatype to be defined,
but as you note, that has been done:

https://github.com/peterjc/galaxy_blast/commit/65252ee61fdd98e52454ff045fa069f04ec40c06

According to the minimal notes I made on the issue for finishing
the PSI BLAST wrapper, it is just help text and unit tests needed
(which would include active user testing):

https://github.com/peterjc/galaxy_blast/issues/19

If you are a PSI BLAST user, it would be very helpful to have
your input here.

Right now the wrapper is on the TravisCI blacklist because
it would fail testing. Likewise it is not included in the Tool Shed.

Peter

On Wed, Feb 1, 2017 at 9:47 AM, De paiva Alves, Eduardo
 wrote:
Peter

I noticed there is now a PSSM datatype which is used by NCBI BLAST+
makeprofiledb. Does that allow you to remove psiblast from blacklist in
your repository?


https://github.com/peterjc/galaxy_blast/blob/13d5b6deca0663d7f1301428574720
b19aea1380/.tt_blacklist


Thank you

Eduardo


On Tue, Feb 5, 2013 at 4:28 PM, Peter Cock <[hidden email]> wrote:
Thanks Luobin,

I've checked that into my development repository (on my tools branch):
https://bitbucket.org/peterjc/galaxy-central/commits/f8f43f8494abdd228998d4
e9fe67b0f2378494e0

That will allow me to track changes etc as we work on the datatypes.
Note I am not yet including ncbi_psiblast_wrapper.xml on the Galaxy
Tool Shed.

Regards,

Peter



The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683
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Re: [galaxy-dev] Tools using Galaxy's Python library?

[Peter Cock]

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_sequence_utils-1.0.1-st.tgz

Commit:

https://github.com/peterjc/pico_galaxy/commit/c9b77b49281974988c790a54f05c4d1ff81b0904

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

Peter

On Wed, Feb 1, 2017 at 9:46 AM, Peter Cock  wrote:
> 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  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 
>> wrote:
>>>
>>> Thanks Nicola,
>>>
>>> I didn't spot the missing slash, but planemo lint did - for anyone
>>> else copy-and-pasting:
>>>
>>> >> version="1.0.1">galaxy_sequence_utils
>>>
>>> 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:
>>>
>>> 
>>> >> />
>>> 
>>>
>>> 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 
>>> wrote:
>>> > Hi Peter,
>>> > adding
>>> >
>>> > >> > version="1.0.1">galaxy_sequence_utils
>>> >
>>> > 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
>>> >>
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Re: [galaxy-dev] psiblast

[Peter Cock]

Hi Eduardo,

Certainly when Luobin Yang submitted the early work on the
PSI BLAST wrapper we need the PSSM datatype to be defined,
but as you note, that has been done:

https://github.com/peterjc/galaxy_blast/commit/65252ee61fdd98e52454ff045fa069f04ec40c06

According to the minimal notes I made on the issue for finishing
the PSI BLAST wrapper, it is just help text and unit tests needed
(which would include active user testing):

https://github.com/peterjc/galaxy_blast/issues/19

If you are a PSI BLAST user, it would be very helpful to have
your input here.

Right now the wrapper is on the TravisCI blacklist because
it would fail testing. Likewise it is not included in the Tool Shed.

Peter

On Wed, Feb 1, 2017 at 9:47 AM, De paiva Alves, Eduardo
 wrote:
> Peter
>
> I noticed there is now a PSSM datatype which is used by NCBI BLAST+
> makeprofiledb. Does that allow you to remove psiblast from blacklist in
> your repository?
>
> https://github.com/peterjc/galaxy_blast/blob/13d5b6deca0663d7f1301428574720
> b19aea1380/.tt_blacklist
>
>
> Thank you
>
> Eduardo
>
>
> On Tue, Feb 5, 2013 at 4:28 PM, Peter Cock <[hidden email]> wrote:
> Thanks Luobin,
>
> I've checked that into my development repository (on my tools branch):
> https://bitbucket.org/peterjc/galaxy-central/commits/f8f43f8494abdd228998d4
> e9fe67b0f2378494e0
>
> That will allow me to track changes etc as we work on the datatypes.
> Note I am not yet including ncbi_psiblast_wrapper.xml on the Galaxy
> Tool Shed.
>
> Regards,
>
> Peter
>
>
>
> The University of Aberdeen is a charity registered in Scotland, No SC013683.
> Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. 
> SC013683.
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[galaxy-dev] psiblast

[De paiva Alves, Eduardo]

Peter

I noticed there is now a PSSM datatype which is used by NCBI BLAST+
makeprofiledb. Does that allow you to remove psiblast from blacklist in
your repository?

https://github.com/peterjc/galaxy_blast/blob/13d5b6deca0663d7f1301428574720
b19aea1380/.tt_blacklist


Thank you

Eduardo


On Tue, Feb 5, 2013 at 4:28 PM, Peter Cock <[hidden email]> wrote:
Thanks Luobin,

I've checked that into my development repository (on my tools branch):
https://bitbucket.org/peterjc/galaxy-central/commits/f8f43f8494abdd228998d4
e9fe67b0f2378494e0

That will allow me to track changes etc as we work on the datatypes.
Note I am not yet including ncbi_psiblast_wrapper.xml on the Galaxy
Tool Shed.

Regards,

Peter



The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. 
SC013683.
___
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Re: [galaxy-dev] Tools using Galaxy's Python library?

[Peter Cock]

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  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 
> wrote:
>>
>> Thanks Nicola,
>>
>> I didn't spot the missing slash, but planemo lint did - for anyone
>> else copy-and-pasting:
>>
>> > version="1.0.1">galaxy_sequence_utils
>>
>> 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:
>>
>> 
>> > />
>> 
>>
>> 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 
>> wrote:
>> > Hi Peter,
>> > adding
>> >
>> > > > version="1.0.1">galaxy_sequence_utils
>> >
>> > 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
>> >>
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