updated nmr tools: nmrmlconv, rnmr1d, speaq; removed: nmr soap tools,…

[c-ruttkies]

… nmrglue

Recycled old nmr tools (soap, nmrglue) and updated new ones (speaq, rnmr1d, nmrmlconv). Galaxy starts but NMR workflow still has problems as nmrml1d is failing. Fix is required here for rnmr1d and a change of the release version needed afterwards in phenomenal_tools2container.yaml.

Please do not merge until fixed. See error message in the comments.

@korseby @djacob65

[c-ruttkies]

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Rnmr1D: Generate the final matrix of spectra... Rnmr1D: Rnmr1D: Write the spec.pack file ... Rnmr1D: Write the list_pars.txt file ... Rnmr1D: used (Mb) gc trigger (Mb) max used (Mb) Ncells 1407522 75.2 2164898 115.7 2164898 115.7 Vcells 1423723 10.9 66719470 509.1 82305555 628.0 user system elapsed 566.380 13.049 773.718 Rnmr1D: ------------------------------------ Rnmr1D: Process the Macro-commands file Rnmr1D: ------------------------------------ Rnmr1D: Rnmr1D: Baseline Correction: PPM Range = ( -0.499979640386268 , 10.9998612451513 ) Rnmr1D: Type=Global - Smoothing Parameter=75 - Window Size=52.5 Rnmr1D: Baseline Correction: PPM Range = ( 2.963 , 4.72 ) Rnmr1D: Type=airPLS, lambda= 1 Error in { : task 1 failed - "missing value where TRUE/FALSE needed" Calls: system.time ... RProcCMD1D -> RairPLSbc1D -> %dopar% -> Timing stopped at: 205.3 8.693 24.23 Execution halted cat: /data/output/data_matrix.txt: No such file or directory

[korseby]

The error produced by rnmr1d should be in issues... Anyway. I contacted Daniel J. Hopefully he has an idea what's causing the error.

[djacob65]

There was not a real bug in the rnmr1d module. In its new version (1.2.22), the rnmr1d module takes into account of the "irradiation frequency offset" acquisition parameter and this for each vendor ("O1" for Bruker, "tof" Varian, "x_offset" for Jeol). This acquisition parameter is the center of the spectral region to be acquired and it is useful (if not essential) to rebuild the ppm scale. But I forgot to extend the nmrML model (XSD). It was why that the preprocessing based on this new version from the previously generated nmrML files without including the "irradiation frequency offset" acquisition parameter produced spectra with a wrong ppm scale. Some process having attempted to deal with ppm zones with all intensities at zero have generated errors.

Now all is fixed, tested and updated. Daniel J

---------------------------------------

I've updated several sources & online applications:

The online nmrML documention - See

http://nmrml.org/schema/v1.0.rc1/doc/doc/schema.html#AcquisitionDimensionParameterSetType

the Java based nmrML converter on github.com/nmrML/

https://github.com/nmrML/nmrML/tree/master/tools/Parser_and_Converters/Java/converter/bin

the online "Vendor to nmrML Converter"

http://nmrml.org/converter/

the Rnmr1D source on bitbucket.org

https://bitbucket.org/nmrprocflow/rnmr1d/

the MTBLS1 datatset in the nmrML format (ZIP) on bitbucket.org

https://bitbucket.org/nmrprocflow/rnmr1d-example/raw/816de03a0c4848949027e8e04a16528552c2c110/input/MTBLS1_nmrML.zip

[korseby]

Thank you very much @djacob65 for the timely changes.

Hi @c-ruttkies , I updated the containers for nmrmlconv & rnmr1d (master branch).

I also updated the container versions in the Galaxy config.

see this commit: https://github.com/c-ruttkies/container-galaxy-k8s-runtime/commit/feb3cc398ced595ef4260cb98f65a3926f4c2e00

Can you have a look?

[djacob65]

@korseby, @c-ruttkies : In https://github.com/phnmnl/container-nmrmlconv/blob/develop/Dockerfile you must replace the revision id in line 8 by the newer

line 8: ENV REVISION="6486b3c0d78cfd6c04d5e96236146ba312b2eb2d" New :id: 7461af4925e4f3bf33eb24b96684a42f68bb2709

Don't forget to regenerate a new MTBLS1_nmrML.zip before trying a new test ! Best

[korseby]

has already been fixed in the master branch - which is being taken for the release

https://github.com/phnmnl/container-nmrmlconv/blob/master/Dockerfile

[djacob65]

@korseby Cool!

Le lun. 25 juin 2018 à 22:10, korseby notifications@github.com a écrit :

has already been fixed in the master branch - which is being taken for the release

https://github.com/phnmnl/container-nmrmlconv/blob/master/Dockerfile

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[korseby]

Hi @rrueedi , concerning metabomatching, I merged develop to master, triggered a new build in jenkins and updated the version tag of the container in Galaxy to v0.2.1_cv0.4.1.66.