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chhh / MSFTBX

MS File ToolBox - tools for parsing some mass-spectrometry related file formats (mzML, mzXML, pep.xml, prot.xml, etc.)
Apache License 2.0
12 stars 4 forks source link

would it be possible to have access to this library in a dependency management framework #1

Closed berlinguyinca closed 8 years ago

berlinguyinca commented 8 years ago

hi,

we would love to work and play with this library. Is it somewhere accessible in a maven repository or so?

kind regards,

Gert

chhh commented 8 years ago

Sorry, missed your question. The library is not in Maven central or any other repository, one of the reasons - it uses a library that I had to modify to make it do what I needed (Javolution), so you won't be able to just set up dependencies on those projects from Central anyways. You have two options:

So all in all - the simplest way is to just get the jars and use them in your project.

chhh commented 8 years ago

@berlinguyinca Also, did you have a chance to try it out already maybe? If you think this will be useful, we can try setting up a repo for easier Maven/Gradle/Ivy integration.

berlinguyinca commented 8 years ago

thank you, we ended up writing our own parsers for mzxml, etc.

g.

On Wed, Aug 24, 2016 at 1:55 PM, Dmitry Avtonomov notifications@github.com wrote:

Sorry, missed your question. The library is not in Maven central or any other repository, one of the reasons - it uses a library that I had to modify to make it do what I needed (Javolution), so you won't be able to just set up dependencies on those projects from Central anyways. You have two options:

  • the Releases https://github.com/chhh/MSFTBX/releases section has precompiled binaries both with and without the dependencies. Just use those jars directly or put them in your local Maven repo.
  • the code is under Apache 2.0, so you can just copy the sources to your tree and add the required dependencies to the project as well (the dependencies are documented in README.md). For Javolution you'll need to use this one - https://github.com/chhh/javolution, you can also just copy the sources to your tree.

So all in all - the simplest way is to just get the jars and use them in your project.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/chhh/MSFTBX/issues/1#issuecomment-242205191, or mute the thread https://github.com/notifications/unsubscribe-auth/AAA_7H8lNlt2siSglXMKLexFul5jDKk9ks5qjK_QgaJpZM4JeJP9 .

Lead Developer - Fiehnlab, UC Davis

gert wohlgemuth

work: http://fiehnlab.ucdavis.edu/staff/wohlgemuth

phone: 530 665 9477

coding blog: http://codingandmore.blogspot.com

linkedin: http://www.linkedin.com/profile/view?id=28611299&trk=tab_pro

berlinguyinca commented 8 years ago

no it sadly was to much work to integrate and keep track of version of jars, etc.

On Wed, Aug 24, 2016 at 1:58 PM, Dmitry Avtonomov notifications@github.com wrote:

@berlinguyinca https://github.com/berlinguyinca Also, did you have a chance to try it out already maybe? If you think this will be useful, we can try setting up a repo for easier Maven/Gradle/Ivy integration.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chhh/MSFTBX/issues/1#issuecomment-242205977, or mute the thread https://github.com/notifications/unsubscribe-auth/AAA_7HUmDdZcIdV9bmG9Al--TmxKbs5nks5qjLB7gaJpZM4JeJP9 .

Lead Developer - Fiehnlab, UC Davis

gert wohlgemuth

work: http://fiehnlab.ucdavis.edu/staff/wohlgemuth

phone: 530 665 9477

coding blog: http://codingandmore.blogspot.com

linkedin: http://www.linkedin.com/profile/view?id=28611299&trk=tab_pro

chhh commented 8 years ago

@berlinguyinca Are your parsers open source? I'd be very much interested in taking a look.

berlinguyinca commented 8 years ago

they will be in a later version, right now it's closed source till we publish.

On Wed, Aug 24, 2016 at 2:02 PM, Dmitry Avtonomov notifications@github.com wrote:

@berlinguyinca https://github.com/berlinguyinca Are your parsers open source? I'd be very much interested in taking a look.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chhh/MSFTBX/issues/1#issuecomment-242206888, or mute the thread https://github.com/notifications/unsubscribe-auth/AAA_7KB0NDC_-KROFWrllWAoOGFKmU9eks5qjLFNgaJpZM4JeJP9 .

Lead Developer - Fiehnlab, UC Davis

gert wohlgemuth

work: http://fiehnlab.ucdavis.edu/staff/wohlgemuth

phone: 530 665 9477

coding blog: http://codingandmore.blogspot.com

linkedin: http://www.linkedin.com/profile/view?id=28611299&trk=tab_pro

chhh commented 8 years ago

@berlinguyinca What publication should I be looking out for? Don't want to miss mass-spec + java stuff.

berlinguyinca commented 8 years ago

its a long time out. Ask me in a year or 2, but something might be of interest for you is the splash project ( https://github.com/berlinguyinca/spectra-hash ,publication pending in nature), the msdk project (https://msdk.github.io/ by tomas pluskal) and the massbank of northern america, which is under heavy development and a better, faster working version to be released in the next 2 weeks. http://mona.fiehnlab.ucdavis.edu

On Wed, Aug 24, 2016 at 2:08 PM, Dmitry Avtonomov notifications@github.com wrote:

@berlinguyinca https://github.com/berlinguyinca What publication should I be looking out for? Don't want to miss mass-spec + java stuff.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chhh/MSFTBX/issues/1#issuecomment-242208591, or mute the thread https://github.com/notifications/unsubscribe-auth/AAA_7KjsqhM8d7Jryi6TReoiVmQO-7PYks5qjLLIgaJpZM4JeJP9 .

Lead Developer - Fiehnlab, UC Davis

gert wohlgemuth

work: http://fiehnlab.ucdavis.edu/staff/wohlgemuth

phone: 530 665 9477

coding blog: http://codingandmore.blogspot.com

linkedin: http://www.linkedin.com/profile/view?id=28611299&trk=tab_pro

chhh commented 8 years ago

@berlinguyinca thanks for the info, the Splash algorithm sounds interesting, will wait for the publication to get the details!