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diann 1.8.1 -> 1.9.1dev #389

Merged
merged 17 commits into from
Jul 23, 2024
Merged

diann 1.8.1 -> 1.9.1dev #389

merged 17 commits into from
Jul 23, 2024

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daichengxin
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/quantms branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jul 22, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2e2f0aa

+| ✅ 292 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-23 01:13:27

This was linked to issues Jul 22, 2024
quantms DIANN 1.9.1dev #380
Closed
Do not upload mzmls on GitHub Actions. Instead upload meaningful intermediate data #383
Closed
jpfeuffer
jpfeuffer reviewed Jul 22, 2024
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jpfeuffer
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@ypriverol ypriverol requested review from jpfeuffer and ypriverol July 23, 2024 08:25
@ypriverol ypriverol self-requested a review July 23, 2024 11:00
@jpfeuffer jpfeuffer removed a link to an issue Jul 23, 2024
Do not upload mzmls on GitHub Actions. Instead upload meaningful intermediate data #383
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@ypriverol ypriverol merged commit 85f04b8 into bigbio:dev Jul 23, 2024
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@wfondrie
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wfondrie commented Jul 31, 2024 •
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Was there an update to the DIANN license that changed the previous conclusion here (#381 (comment))?

We are closing this PR. In the current LICENSE of DIANN, cloud infrastructures are not allowed.

@wfondrie
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@ypriverol - this is the contents of the license distributed with https://github.com/vdemichev/DiaNN/releases/tag/1.9.1:

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA,
OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Herein the terms 'DIA-NN' or 'DIA-NN software' are used to refer to specifically the
version of the DIA-NN software which packs this license file in its distribution package.

  1. Special DIA-NN software usage scenarious.
    Collaborative use refers to any usage of the DIA-NN software solely for the purpose of
    carrying out a joint collaborative project between yourself or your insititution and the Demichev
    laboratory at the Charité – Universitätsmedizin Berlin. The nature of the project and the intended
    use of the DIA-NN software in this case must be agreed with the Demichev laboratory in advance.

  2. The DIA-NN software is licensed to you for use only under the terms of this License,
    and all rights not expressly granted to you are reserved. The rights granted herein are limited to Vadim Demichev’s intellectual
    property rights in the DIA-NN software and do not include any other patents or intellectual property rights.

  3. Permitted use. Provided the usage restrictions imposed by this License are satisfied,
    this License allows you to install and use the DIA-NN software either (i) solely for the purpose of
    academic research or education or (ii) under the Collaborative use usage scenario or
    (iii) solely for the purpose of publishing a benchmark that either demonstrates the performance
    of a particular method / technology / data analysis approach or demonstrates the qualities of a particular data set.
    You may make one copy of the DIA-NN software in machine-readable form for backup purposes only,
    provided that the backup copy must include all copyright or other proprietary notices contained on the original.
    Usage of DIA-NN in the cloud is only permitted under Collaborative use. Except as and only to the extent expressly
    permitted in this License or by applicable law, you may not copy, decompile, reverse engineer, disassemble,
    attempt to derive the source code of, modify, or create derivative works of the DIA-NN software or any part thereof.

  4. Transfer. You may not rent, lease, lend or sublicense the DIA-NN software. You may, however, make a one-time permanent transfer
    of all of your license rights to the DIA-NN software to another party, provided that: (a) the transfer must include all of the DIA-NN software,
    including all its component parts, original media, printed materials and this License; (b) you do not retain any copies of the DIA-NN software,
    full or partial, including copies stored on a computer or other storage device; and (c) the party receiving the DIA-NN software reads
    and agrees to accept the terms and conditions of this License.

  5. Attribution. If you share, distribute or publish any materials that were produced using the DIA-NN software ("Derived Materials"), you must indicate
    within these Derived Materials that they were produced using the DIA-NN software. You may satisfy this condition in any reasonable manner
    based on the medium, means, and context in which you share the Derived Materials. For example, the required attribution can be expressed by including
    one of the statements "Processed using DIA-NN", "Generated using DIA-NN" or "Produced using DIA-NN" in the Derived Materials.

  6. All third-party software included in this DIA-NN software distribution retains its original license.
    For the inclusion in this DIA-NN software distribution, the source code of MSToolkit and MiniDNN was modified.
    If not packaged within this distribution, please find the source code of the third-party software at https://github.com/vdemichev/DiaNN
    or at the respective website of the third-party software.

  7. Experimental functionality.
    Any of the DIA-NN commands/options that are not referenced at https://github.com/vdemichev/DiaNN/blob/master/README.md
    are considered Experimental functionality. The following DIA-NN commands/options are also considered Experimental functionality:
    --extract
    --mgf
    Experimental functionality is in the process of being actively developed and is thus shared 'on collaborative basis'
    before it is published in a peer-reviewed publication. It is not tested as thoroughly as the rest of DIA-NN and
    needs to be used with caution, with expertise in the internal workings of DIA-NN potentially required for correct use.
    Any peer-reviewed publication or academic preprint derived from any usage of Experimental functionality that occurs
    before a peer-reviewed manuscript describing the respective Experimental functionality is published must therefore
    be published in collaboration and co-authorship with the Demichev laboratory. Using Experimental functionality is not
    permitted if you do not agree to the above. A peer-reviewed manuscript is considered to describe a particular
    Experimental functionality if (i) it is referenced at https://github.com/vdemichev/DiaNN/blob/master/README.md
    as describing this functionality and (ii) the date when it was made available online by the publisher falls after
    the date on which the specific version of the DIA-NN software to which this license refers to was built.

A couple key provisions will prevent us from using quantms going forward unless the version is reverted:

  1. Commercial use is not granted:

this License allows you to install and use the DIA-NN software either (i) solely for the purpose of
academic research or education or (ii) under the Collaborative use usage scenario or
(iii) solely for the purpose of publishing a benchmark that either demonstrates the performance
of a particular method / technology / data analysis approach or demonstrates the qualities of a particular data set.

  1. Only collaborators can run DIANN in the cloud:

Usage of DIA-NN in the cloud is only permitted under Collaborative use.

@ypriverol
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ypriverol commented Jul 31, 2024 •
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I discussed with @vdemichev and the license explicitly said that cloud use (for me meaning docker in the context of quantms) is not allowed even in an academic context. Then, we have decided to support only singularity.

Probably @vdemichev can make everything more clear in the issue. Singularity will allow the users to run it locally, and also in HPC infrastructure.

We will add in the release the DIANN License in the main repo. Currently, 1.8.1 is the default and only 1.9.1 is available for those that can fulfil the requirements.

@wfondrie
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Thanks @ypriverol! Sorry I was quick to respond before diving into the contents of this PR.

@ypriverol
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It is fine. This topic is complex because also docker can be used locally but the main advantage is to use it in the cloud and because the cloud is now "not permitted", we can't be enablers of it.

@jpfeuffer
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Yes we explicitly decided to default to 1.8.1 due to the license, right @ypriverol ?

For 1.8.1 we support the biocontainer images for docker and singularity.

But people that want to try the new version can do so now with a custom singularity image.
Personally I would have been fine with just fixing the parsing scripts and letting the user overwrite the config everytime but here we introduce a parameter that automatically picks the right image etc.

By the way @ypriverol We should probably print an error if the "backend" is AWS/AWS batch with this version.

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@ypriverol ypriverol ypriverol approved these changes

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quantms DIANN 1.9.1dev
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@daichengxin @wfondrie @ypriverol @jpfeuffer