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Posted to dev@taverna.apache.org by Stian Soiland-Reyes <st...@apache.org> on 2014/11/20 12:04:30 UTC
Re: Taverna .deb -> apt-getable repository - finally
On 20 November 2014 10:54, "Steffen Möller" <st...@gmx.de> wrote:
> Hi Stian,
>
> Tim and I are here at this EDAM-put-your-stuff-in Hackathon in Copenhagen and ... guess what ... we think off you and your Taverna .deb awaiting to be homed in an apt-get-able repository. You may recall that I claimed this all to be easy and then nothing worked for me ... Tim, having his .deb repository for ages, confirmed that it should be easy and hat it at his fingertips:
>
> sudo apt-get install apt-utils # for apt-ftparchive
>
> mkdir taverna/repository
> cd taverna/repository
> wget
/taverna-workbench-core-2.5.0-linux_amd64.deb
> apt-ftparchive packages . |tee ../Packages | gzip -c9n > ../Packages.gz
> cd ..
> apt-ftparchive release .|tee Release
> gpg --detach-sign -a Release
> mv Release.asc Release.gpg
>
> We found
> https://wiki.debian.org/HowToSetupADebianRepository#apt-ftparchive
> with some google search that may help any further decision making on your side ...
> For any issues arising please contact Tim who easily finds his BioLinux scripts once he is back at his servers.
Great! That seems fairly easy - as long as I am able to create the
repository on a Debian machine and then transfer it across to our
awkward Fedora server :)
So your suggestion is we put this repository at the Taverna update
site, or you have already created one?
You would probably want to use the alternative *.deb files that I
asked for someone to test in Ubuntu (which didn't get any response) -
see
http://updates.taverna.org.uk/tmp/2.5.0-T3-1207/
We should definitely try to do such a repository for the 2.5.1
("final" Non-Apache) release.
Apache Mentors - do you know of other projects that do Debian
repositories for their stuff - or feed into the main repositories?
BTW, Steffen, have you signed up to
https://mail-archives.apache.org/mod_mbox/incubator-taverna-dev/ ?
--
Stian Soiland-Reyes
Apache Taverna (incubating)
http://orcid.org/0000-0001-9842-9718
Re: Taverna .deb -> apt-getable repository - finally
Posted by Marlon Pierce <ma...@iu.edu>.
I don't but checking out other Apache projects is always a good place to
start.
Marlon
On 11/27/14, 4:24 PM, Stian Soiland-Reyes wrote:
> (Mentors - do you have any knowledge of OS-specific installers and JRE
> bundling in other Apache projects)
>
> Yes, the JavaFX installers are noteworthy. I did look at that at some
> point.
>
> In my opinion It would be a mess to build for 2.x line if it is true what
> you say, although with enough virtual machines and Jenkins slaves it could
> be possible. One hidden reason for moving to Apache was to be less reliant
> on that kind of infrastructure, but perhaps Jenkins at Apache already has
> this setup available?
>
> We currently make binaries for Windows x64, i386, OS X, Linux RPM, DEB and
> a "platforms neutral" zip. This is done by a single Maven build of the
> taverna-workbench-product (and taverna-command-line product). Then this was
> for 2.5 repeated for each edition as a branch of the product (for 3.0 the
> separate edition downloads should not be needed), so each edition build
> output all its installers.
>
> All variants (except the zip) bundle OpenJDK 7 (only JRE) and Graphviz (in
> Workbench) as we found users struggle to install these things manually
> these days - particularly on macs (not helped by OS vendors locking
> everything down ).
>
> We bundled OpenJDK instead of Oracle's JRE as
> 1) it was compatible with LGPL if upgraded to GPL (as happens in Astronomy
> Taverna)
> 2) it comes with strong cryptography turned on by default, which is used by
> Credential Manager. (Workaround? Passphrase must be 6 characters or less..)
>
> For Apache 3.0 I doubt we can bundle OpenJDK (GPL with class path
> exception) - but should be more free to bundle normal JRE (Apache
> OpenOffice does this I believe). It would be sad to loose the Strong
> cryptography by default, but as Taverna now use have a default passphrase
> that is short enough, most people wouldn't notice. (check: did that new
> default password make it into the 3.0 branch?)
>
> I have assumed we can keep using Install4j under Apache, but it is probably
> good if anyone of you could contact him to verify. (Volunteers?) The
> author is a really nice guy. His only requirement was that we have a Thank
> You note on the website, which Apache allows (if done in a neutral way).
> Our old note: http://www.taverna.org.uk/about/tools-we-use/
> On 27 Nov 2014 17:56, "Mark Fortner" <ph...@gmail.com> wrote:
>
>> Stian,
>>
>> Just out of curiosity, have you looked at the JavaFX packaging tools? They
>> can be used to package Swing applications and create native installers. The
>> only caveat is that you currently can only package on your target platform.
>> So if you're deploying to Ubuntu on amd64, you have to be building on that
>> platform.
>>
>> https://docs.oracle.com/javafx/2/deployment/deploy_swing_apps.htm
>>
>> Mark
>> On Nov 26, 2014 9:04 AM, "Stian Soiland-Reyes" <
>> soiland-reyes@cs.manchester.ac.uk> wrote:
>>
>>> We've just been relying on Install4J which makes the .deb using its own
>>> code rather than deb tools, as the installers can be built on my host OS.
>>>
>>> It is unclear if we can keep using Install4j (proprietary with free
>> license
>>> for open source projects) under Apache, but we should anyway still use it
>>> for 2.5.1, and I don't see any harm in making such a repository even if
>>> there won't be any updates of 2.x beyond 2.5.1.
>>>
>>> Thanks for figuring this out!
>>> On 26 Nov 2014 16:48, "Tim Booth" <tb...@ceh.ac.uk> wrote:
>>>
>>>> I sent this on Monday and got a delivery failure. Trying again. Sorry
>>>> if you get it twice.
>>>>
>>>> TIM
>>>>
>>>> ===
>>>>
>>>> Hi,
>>>>
>>>> I just wanted to add one piece of advice regarding setting up a Debian
>>>> repo for the DEB packages. Once you have worked out where to put the
>>>> output of apt-ftparchive and how to sign the release with GPG you are
>>>> basically there, but when updating the archive remember this -
>>>>
>>>> APT gets rather upset if there are two packages with the same version
>>>> that are not binary-identical. So ensure that if you make even the
>>>> tiniest change to a package you bump the package revision number (ie.
>>>> the part of the version string following the hyphen).
>>>>
>>>> Also, the way APT decides which of two version numbers is the larger is
>>>> rather complicated, so bear this in mind. For example:
>>>>
>>>> 1.8 < 1.9
>>>> 1.9 < 1.10 (as you would expect)
>>>> 1.0rc1 < 1.0.0 (RC is followed by final release)
>>>>
>>>> but
>>>>
>>>> 1.0.rc1 > 1.0.0 (probably not what you wanted)
>>>> 1.0rc1 > 1.0 (ditto)
>>>>
>>>> Also, small errors in the control file can really upset APT and make it
>>>> behave erratically (eg. updating a package repeatedly even though it
>> has
>>>> not changed). When you build from source packages this all gets
>> checked
>>>> for you but here you have bypassed all that and so have to be careful.
>>>>
>>>> If you need any help getting the repo working just let me know. Now
>> I'm
>>>> back in the office I can actually get to the machine with the build
>>>> scripts on to remind myself exactly how things work.
>>>>
>>>> Cheers,
>>>>
>>>> TIM
>>>>
>>>> On Thu, 2014-11-20 at 14:18 +0000, alaninmcr wrote:
>>>>> On 20/11/2014 13:13, "Steffen Möller" wrote:
>>>>>> Hi Alan,
>>>>>>
>>>>>>> I guess it should be separate packages for the variants of Taverna
>>> 2.5
>>>>>>> e.g. biodiversity and astronomy.
>>>>>> Once you have the repository set up, it will all become easy to
>> split
>>>> things
>>>>>> up for a better user experience.
>>>>> OK. The variants are currently available as separate .deb downloads
>>>>>
>>>>>>> Steffen, on a side issue, have you been tracking the common
>> workflow
>>>>>>> language group's work on developing tool descriptions?
>>>>>> No, I have not, but am happy for any step forward. I am writing
>> from
>>>>>> the ELIXIR-DK EDAM ontology hackathon and the corresponding catalog
>>>>>> that is to be partially fed by the Debian distro.
>>>>> Very interesting.
>>>>>
>>>>>> Nobody is aware of
>>>>>> those command line interfaces to Taverna or the 2008 Bioinformatics
>>>>>> paper. Scandal! So, I will show the Taverna-ready descriptions of
>>>>>> tool-usages to the catalog people over here and let us see how they
>>>>>> react to it.
>>>>> OK. The common workflow languages group
>>>>> common-workflow-language@googlegroups.com is a public Google group
>>> that
>>>>> includes people from several workflow languages. Despite the name,
>> its
>>>>> initial target is the specification of a format for describing
>> "steps"
>>> -
>>>>> so the tool description of Taverna with more capability.
>>>>>
>>>>> A good place to start is
>>>>>
>>>>> https://github.com/rabix/common-workflow-language/tree/master/core
>> for
>>>>> the specs.
>>>>>
>>>>> Fun things are being done (by other people) about describing docker
>>>> "tools".
>>>>>> Best,
>>>>>>
>>>>>> Steffen
>>>>> Alan
>>>>
>>>> --
>>>> Tim Booth <tb...@ceh.ac.uk>
>>>> NERC Environmental Bioinformatics Centre
>>>>
>>>> Centre for Ecology and Hydrology
>>>> Maclean Bldg, Benson Lane
>>>> Crowmarsh Gifford
>>>> Wallingford, England
>>>> OX10 8BB
>>>>
>>>> http://nebc.nerc.ac.uk
>>>> +44 1491 69 2705
>>>>
Re: Taverna .deb -> apt-getable repository - finally
Posted by Stian Soiland-Reyes <st...@soiland-reyes.com>.
(Mentors - do you have any knowledge of OS-specific installers and JRE
bundling in other Apache projects)
Yes, the JavaFX installers are noteworthy. I did look at that at some
point.
In my opinion It would be a mess to build for 2.x line if it is true what
you say, although with enough virtual machines and Jenkins slaves it could
be possible. One hidden reason for moving to Apache was to be less reliant
on that kind of infrastructure, but perhaps Jenkins at Apache already has
this setup available?
We currently make binaries for Windows x64, i386, OS X, Linux RPM, DEB and
a "platforms neutral" zip. This is done by a single Maven build of the
taverna-workbench-product (and taverna-command-line product). Then this was
for 2.5 repeated for each edition as a branch of the product (for 3.0 the
separate edition downloads should not be needed), so each edition build
output all its installers.
All variants (except the zip) bundle OpenJDK 7 (only JRE) and Graphviz (in
Workbench) as we found users struggle to install these things manually
these days - particularly on macs (not helped by OS vendors locking
everything down ).
We bundled OpenJDK instead of Oracle's JRE as
1) it was compatible with LGPL if upgraded to GPL (as happens in Astronomy
Taverna)
2) it comes with strong cryptography turned on by default, which is used by
Credential Manager. (Workaround? Passphrase must be 6 characters or less..)
For Apache 3.0 I doubt we can bundle OpenJDK (GPL with class path
exception) - but should be more free to bundle normal JRE (Apache
OpenOffice does this I believe). It would be sad to loose the Strong
cryptography by default, but as Taverna now use have a default passphrase
that is short enough, most people wouldn't notice. (check: did that new
default password make it into the 3.0 branch?)
I have assumed we can keep using Install4j under Apache, but it is probably
good if anyone of you could contact him to verify. (Volunteers?) The
author is a really nice guy. His only requirement was that we have a Thank
You note on the website, which Apache allows (if done in a neutral way).
Our old note: http://www.taverna.org.uk/about/tools-we-use/
On 27 Nov 2014 17:56, "Mark Fortner" <ph...@gmail.com> wrote:
> Stian,
>
> Just out of curiosity, have you looked at the JavaFX packaging tools? They
> can be used to package Swing applications and create native installers. The
> only caveat is that you currently can only package on your target platform.
> So if you're deploying to Ubuntu on amd64, you have to be building on that
> platform.
>
> https://docs.oracle.com/javafx/2/deployment/deploy_swing_apps.htm
>
> Mark
> On Nov 26, 2014 9:04 AM, "Stian Soiland-Reyes" <
> soiland-reyes@cs.manchester.ac.uk> wrote:
>
> > We've just been relying on Install4J which makes the .deb using its own
> > code rather than deb tools, as the installers can be built on my host OS.
> >
> > It is unclear if we can keep using Install4j (proprietary with free
> license
> > for open source projects) under Apache, but we should anyway still use it
> > for 2.5.1, and I don't see any harm in making such a repository even if
> > there won't be any updates of 2.x beyond 2.5.1.
> >
> > Thanks for figuring this out!
> > On 26 Nov 2014 16:48, "Tim Booth" <tb...@ceh.ac.uk> wrote:
> >
> > > I sent this on Monday and got a delivery failure. Trying again. Sorry
> > > if you get it twice.
> > >
> > > TIM
> > >
> > > ===
> > >
> > > Hi,
> > >
> > > I just wanted to add one piece of advice regarding setting up a Debian
> > > repo for the DEB packages. Once you have worked out where to put the
> > > output of apt-ftparchive and how to sign the release with GPG you are
> > > basically there, but when updating the archive remember this -
> > >
> > > APT gets rather upset if there are two packages with the same version
> > > that are not binary-identical. So ensure that if you make even the
> > > tiniest change to a package you bump the package revision number (ie.
> > > the part of the version string following the hyphen).
> > >
> > > Also, the way APT decides which of two version numbers is the larger is
> > > rather complicated, so bear this in mind. For example:
> > >
> > > 1.8 < 1.9
> > > 1.9 < 1.10 (as you would expect)
> > > 1.0rc1 < 1.0.0 (RC is followed by final release)
> > >
> > > but
> > >
> > > 1.0.rc1 > 1.0.0 (probably not what you wanted)
> > > 1.0rc1 > 1.0 (ditto)
> > >
> > > Also, small errors in the control file can really upset APT and make it
> > > behave erratically (eg. updating a package repeatedly even though it
> has
> > > not changed). When you build from source packages this all gets
> checked
> > > for you but here you have bypassed all that and so have to be careful.
> > >
> > > If you need any help getting the repo working just let me know. Now
> I'm
> > > back in the office I can actually get to the machine with the build
> > > scripts on to remind myself exactly how things work.
> > >
> > > Cheers,
> > >
> > > TIM
> > >
> > > On Thu, 2014-11-20 at 14:18 +0000, alaninmcr wrote:
> > > > On 20/11/2014 13:13, "Steffen Möller" wrote:
> > > > > Hi Alan,
> > > > >
> > > > >> I guess it should be separate packages for the variants of Taverna
> > 2.5
> > > > >> e.g. biodiversity and astronomy.
> > > > >
> > > > > Once you have the repository set up, it will all become easy to
> split
> > > things
> > > > > up for a better user experience.
> > > >
> > > > OK. The variants are currently available as separate .deb downloads
> > > >
> > > > >> Steffen, on a side issue, have you been tracking the common
> workflow
> > > > >> language group's work on developing tool descriptions?
> > > > >
> > > > > No, I have not, but am happy for any step forward. I am writing
> from
> > > > > the ELIXIR-DK EDAM ontology hackathon and the corresponding catalog
> > > > > that is to be partially fed by the Debian distro.
> > > >
> > > > Very interesting.
> > > >
> > > > > Nobody is aware of
> > > > > those command line interfaces to Taverna or the 2008 Bioinformatics
> > > > > paper. Scandal! So, I will show the Taverna-ready descriptions of
> > > > > tool-usages to the catalog people over here and let us see how they
> > > > > react to it.
> > > >
> > > > OK. The common workflow languages group
> > > > common-workflow-language@googlegroups.com is a public Google group
> > that
> > > > includes people from several workflow languages. Despite the name,
> its
> > > > initial target is the specification of a format for describing
> "steps"
> > -
> > > > so the tool description of Taverna with more capability.
> > > >
> > > > A good place to start is
> > > >
> > > > https://github.com/rabix/common-workflow-language/tree/master/core
> for
> > > > the specs.
> > > >
> > > > Fun things are being done (by other people) about describing docker
> > > "tools".
> > > >
> > > > > Best,
> > > > >
> > > > > Steffen
> > > >
> > > > Alan
> > >
> > >
> > > --
> > > Tim Booth <tb...@ceh.ac.uk>
> > > NERC Environmental Bioinformatics Centre
> > >
> > > Centre for Ecology and Hydrology
> > > Maclean Bldg, Benson Lane
> > > Crowmarsh Gifford
> > > Wallingford, England
> > > OX10 8BB
> > >
> > > http://nebc.nerc.ac.uk
> > > +44 1491 69 2705
> > >
> >
>
Re: Aw: Re: Taverna .deb -> apt-getable repository - finally
Posted by Mark Fortner <ph...@gmail.com>.
Stian,
Just out of curiosity, have you looked at the JavaFX packaging tools? They
can be used to package Swing applications and create native installers. The
only caveat is that you currently can only package on your target platform.
So if you're deploying to Ubuntu on amd64, you have to be building on that
platform.
https://docs.oracle.com/javafx/2/deployment/deploy_swing_apps.htm
Mark
On Nov 26, 2014 9:04 AM, "Stian Soiland-Reyes" <
soiland-reyes@cs.manchester.ac.uk> wrote:
> We've just been relying on Install4J which makes the .deb using its own
> code rather than deb tools, as the installers can be built on my host OS.
>
> It is unclear if we can keep using Install4j (proprietary with free license
> for open source projects) under Apache, but we should anyway still use it
> for 2.5.1, and I don't see any harm in making such a repository even if
> there won't be any updates of 2.x beyond 2.5.1.
>
> Thanks for figuring this out!
> On 26 Nov 2014 16:48, "Tim Booth" <tb...@ceh.ac.uk> wrote:
>
> > I sent this on Monday and got a delivery failure. Trying again. Sorry
> > if you get it twice.
> >
> > TIM
> >
> > ===
> >
> > Hi,
> >
> > I just wanted to add one piece of advice regarding setting up a Debian
> > repo for the DEB packages. Once you have worked out where to put the
> > output of apt-ftparchive and how to sign the release with GPG you are
> > basically there, but when updating the archive remember this -
> >
> > APT gets rather upset if there are two packages with the same version
> > that are not binary-identical. So ensure that if you make even the
> > tiniest change to a package you bump the package revision number (ie.
> > the part of the version string following the hyphen).
> >
> > Also, the way APT decides which of two version numbers is the larger is
> > rather complicated, so bear this in mind. For example:
> >
> > 1.8 < 1.9
> > 1.9 < 1.10 (as you would expect)
> > 1.0rc1 < 1.0.0 (RC is followed by final release)
> >
> > but
> >
> > 1.0.rc1 > 1.0.0 (probably not what you wanted)
> > 1.0rc1 > 1.0 (ditto)
> >
> > Also, small errors in the control file can really upset APT and make it
> > behave erratically (eg. updating a package repeatedly even though it has
> > not changed). When you build from source packages this all gets checked
> > for you but here you have bypassed all that and so have to be careful.
> >
> > If you need any help getting the repo working just let me know. Now I'm
> > back in the office I can actually get to the machine with the build
> > scripts on to remind myself exactly how things work.
> >
> > Cheers,
> >
> > TIM
> >
> > On Thu, 2014-11-20 at 14:18 +0000, alaninmcr wrote:
> > > On 20/11/2014 13:13, "Steffen Möller" wrote:
> > > > Hi Alan,
> > > >
> > > >> I guess it should be separate packages for the variants of Taverna
> 2.5
> > > >> e.g. biodiversity and astronomy.
> > > >
> > > > Once you have the repository set up, it will all become easy to split
> > things
> > > > up for a better user experience.
> > >
> > > OK. The variants are currently available as separate .deb downloads
> > >
> > > >> Steffen, on a side issue, have you been tracking the common workflow
> > > >> language group's work on developing tool descriptions?
> > > >
> > > > No, I have not, but am happy for any step forward. I am writing from
> > > > the ELIXIR-DK EDAM ontology hackathon and the corresponding catalog
> > > > that is to be partially fed by the Debian distro.
> > >
> > > Very interesting.
> > >
> > > > Nobody is aware of
> > > > those command line interfaces to Taverna or the 2008 Bioinformatics
> > > > paper. Scandal! So, I will show the Taverna-ready descriptions of
> > > > tool-usages to the catalog people over here and let us see how they
> > > > react to it.
> > >
> > > OK. The common workflow languages group
> > > common-workflow-language@googlegroups.com is a public Google group
> that
> > > includes people from several workflow languages. Despite the name, its
> > > initial target is the specification of a format for describing "steps"
> -
> > > so the tool description of Taverna with more capability.
> > >
> > > A good place to start is
> > >
> > > https://github.com/rabix/common-workflow-language/tree/master/core for
> > > the specs.
> > >
> > > Fun things are being done (by other people) about describing docker
> > "tools".
> > >
> > > > Best,
> > > >
> > > > Steffen
> > >
> > > Alan
> >
> >
> > --
> > Tim Booth <tb...@ceh.ac.uk>
> > NERC Environmental Bioinformatics Centre
> >
> > Centre for Ecology and Hydrology
> > Maclean Bldg, Benson Lane
> > Crowmarsh Gifford
> > Wallingford, England
> > OX10 8BB
> >
> > http://nebc.nerc.ac.uk
> > +44 1491 69 2705
> >
>
Re: Aw: Re: Taverna .deb -> apt-getable repository - finally
Posted by Stian Soiland-Reyes <so...@cs.manchester.ac.uk>.
We've just been relying on Install4J which makes the .deb using its own
code rather than deb tools, as the installers can be built on my host OS.
It is unclear if we can keep using Install4j (proprietary with free license
for open source projects) under Apache, but we should anyway still use it
for 2.5.1, and I don't see any harm in making such a repository even if
there won't be any updates of 2.x beyond 2.5.1.
Thanks for figuring this out!
On 26 Nov 2014 16:48, "Tim Booth" <tb...@ceh.ac.uk> wrote:
> I sent this on Monday and got a delivery failure. Trying again. Sorry
> if you get it twice.
>
> TIM
>
> ===
>
> Hi,
>
> I just wanted to add one piece of advice regarding setting up a Debian
> repo for the DEB packages. Once you have worked out where to put the
> output of apt-ftparchive and how to sign the release with GPG you are
> basically there, but when updating the archive remember this -
>
> APT gets rather upset if there are two packages with the same version
> that are not binary-identical. So ensure that if you make even the
> tiniest change to a package you bump the package revision number (ie.
> the part of the version string following the hyphen).
>
> Also, the way APT decides which of two version numbers is the larger is
> rather complicated, so bear this in mind. For example:
>
> 1.8 < 1.9
> 1.9 < 1.10 (as you would expect)
> 1.0rc1 < 1.0.0 (RC is followed by final release)
>
> but
>
> 1.0.rc1 > 1.0.0 (probably not what you wanted)
> 1.0rc1 > 1.0 (ditto)
>
> Also, small errors in the control file can really upset APT and make it
> behave erratically (eg. updating a package repeatedly even though it has
> not changed). When you build from source packages this all gets checked
> for you but here you have bypassed all that and so have to be careful.
>
> If you need any help getting the repo working just let me know. Now I'm
> back in the office I can actually get to the machine with the build
> scripts on to remind myself exactly how things work.
>
> Cheers,
>
> TIM
>
> On Thu, 2014-11-20 at 14:18 +0000, alaninmcr wrote:
> > On 20/11/2014 13:13, "Steffen Möller" wrote:
> > > Hi Alan,
> > >
> > >> I guess it should be separate packages for the variants of Taverna 2.5
> > >> e.g. biodiversity and astronomy.
> > >
> > > Once you have the repository set up, it will all become easy to split
> things
> > > up for a better user experience.
> >
> > OK. The variants are currently available as separate .deb downloads
> >
> > >> Steffen, on a side issue, have you been tracking the common workflow
> > >> language group's work on developing tool descriptions?
> > >
> > > No, I have not, but am happy for any step forward. I am writing from
> > > the ELIXIR-DK EDAM ontology hackathon and the corresponding catalog
> > > that is to be partially fed by the Debian distro.
> >
> > Very interesting.
> >
> > > Nobody is aware of
> > > those command line interfaces to Taverna or the 2008 Bioinformatics
> > > paper. Scandal! So, I will show the Taverna-ready descriptions of
> > > tool-usages to the catalog people over here and let us see how they
> > > react to it.
> >
> > OK. The common workflow languages group
> > common-workflow-language@googlegroups.com is a public Google group that
> > includes people from several workflow languages. Despite the name, its
> > initial target is the specification of a format for describing "steps" -
> > so the tool description of Taverna with more capability.
> >
> > A good place to start is
> >
> > https://github.com/rabix/common-workflow-language/tree/master/core for
> > the specs.
> >
> > Fun things are being done (by other people) about describing docker
> "tools".
> >
> > > Best,
> > >
> > > Steffen
> >
> > Alan
>
>
> --
> Tim Booth <tb...@ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://nebc.nerc.ac.uk
> +44 1491 69 2705
>
Re: Aw: Re: Taverna .deb -> apt-getable repository - finally
Posted by Tim Booth <tb...@ceh.ac.uk>.
I sent this on Monday and got a delivery failure. Trying again. Sorry
if you get it twice.
TIM
===
Hi,
I just wanted to add one piece of advice regarding setting up a Debian
repo for the DEB packages. Once you have worked out where to put the
output of apt-ftparchive and how to sign the release with GPG you are
basically there, but when updating the archive remember this -
APT gets rather upset if there are two packages with the same version
that are not binary-identical. So ensure that if you make even the
tiniest change to a package you bump the package revision number (ie.
the part of the version string following the hyphen).
Also, the way APT decides which of two version numbers is the larger is
rather complicated, so bear this in mind. For example:
1.8 < 1.9
1.9 < 1.10 (as you would expect)
1.0rc1 < 1.0.0 (RC is followed by final release)
but
1.0.rc1 > 1.0.0 (probably not what you wanted)
1.0rc1 > 1.0 (ditto)
Also, small errors in the control file can really upset APT and make it
behave erratically (eg. updating a package repeatedly even though it has
not changed). When you build from source packages this all gets checked
for you but here you have bypassed all that and so have to be careful.
If you need any help getting the repo working just let me know. Now I'm
back in the office I can actually get to the machine with the build
scripts on to remind myself exactly how things work.
Cheers,
TIM
On Thu, 2014-11-20 at 14:18 +0000, alaninmcr wrote:
> On 20/11/2014 13:13, "Steffen Möller" wrote:
> > Hi Alan,
> >
> >> I guess it should be separate packages for the variants of Taverna 2.5
> >> e.g. biodiversity and astronomy.
> >
> > Once you have the repository set up, it will all become easy to split things
> > up for a better user experience.
>
> OK. The variants are currently available as separate .deb downloads
>
> >> Steffen, on a side issue, have you been tracking the common workflow
> >> language group's work on developing tool descriptions?
> >
> > No, I have not, but am happy for any step forward. I am writing from
> > the ELIXIR-DK EDAM ontology hackathon and the corresponding catalog
> > that is to be partially fed by the Debian distro.
>
> Very interesting.
>
> > Nobody is aware of
> > those command line interfaces to Taverna or the 2008 Bioinformatics
> > paper. Scandal! So, I will show the Taverna-ready descriptions of
> > tool-usages to the catalog people over here and let us see how they
> > react to it.
>
> OK. The common workflow languages group
> common-workflow-language@googlegroups.com is a public Google group that
> includes people from several workflow languages. Despite the name, its
> initial target is the specification of a format for describing "steps" -
> so the tool description of Taverna with more capability.
>
> A good place to start is
>
> https://github.com/rabix/common-workflow-language/tree/master/core for
> the specs.
>
> Fun things are being done (by other people) about describing docker "tools".
>
> > Best,
> >
> > Steffen
>
> Alan
--
Tim Booth <tb...@ceh.ac.uk>
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://nebc.nerc.ac.uk
+44 1491 69 2705
Re: Aw: Re: Taverna .deb -> apt-getable repository - finally
Posted by alaninmcr <al...@googlemail.com>.
On 20/11/2014 13:13, "Steffen Möller" wrote:
> Hi Alan,
>
>> I guess it should be separate packages for the variants of Taverna 2.5
>> e.g. biodiversity and astronomy.
>
> Once you have the repository set up, it will all become easy to split things
> up for a better user experience.
OK. The variants are currently available as separate .deb downloads
>> Steffen, on a side issue, have you been tracking the common workflow
>> language group's work on developing tool descriptions?
>
> No, I have not, but am happy for any step forward. I am writing from
> the ELIXIR-DK EDAM ontology hackathon and the corresponding catalog
> that is to be partially fed by the Debian distro.
Very interesting.
> Nobody is aware of
> those command line interfaces to Taverna or the 2008 Bioinformatics
> paper. Scandal! So, I will show the Taverna-ready descriptions of
> tool-usages to the catalog people over here and let us see how they
> react to it.
OK. The common workflow languages group
common-workflow-language@googlegroups.com is a public Google group that
includes people from several workflow languages. Despite the name, its
initial target is the specification of a format for describing "steps" -
so the tool description of Taverna with more capability.
A good place to start is
https://github.com/rabix/common-workflow-language/tree/master/core for
the specs.
Fun things are being done (by other people) about describing docker "tools".
> Best,
>
> Steffen
Alan
Aw: Re: Taverna .deb -> apt-getable repository - finally
Posted by Steffen Möller <st...@gmx.de>.
Hi Alan,
> I guess it should be separate packages for the variants of Taverna 2.5
> e.g. biodiversity and astronomy.
Once you have the repository set up, it will all become easy to split things
up for a better user experience.
>
> Steffen, on a side issue, have you been tracking the common workflow
> language group's work on developing tool descriptions?
No, I have not, but am happy for any step forward. I am writing from
the ELIXIR-DK EDAM ontology hackathon and the corresponding catalog
that is to be partially fed by the Debian distro. Nobody is aware of
those command line interfaces to Taverna or the 2008 Bioinformatics
paper. Scandal! So, I will show the Taverna-ready descriptions of
tool-usages to the catalog people over here and let us see how they
react to it.
Best,
Steffen
Re: Taverna .deb -> apt-getable repository - finally
Posted by alaninmcr <al...@googlemail.com>.
Hello everybody,
Steffen, that is great news.
I guess it should be separate packages for the variants of Taverna 2.5
e.g. biodiversity and astronomy.
Steffen, on a side issue, have you been tracking the common workflow
language group's work on developing tool descriptions?
Alan