Install trouble - nextflow incompatible packages

[tjlundgren]

Hello,
I was hoping to try your software locally, but ran into some issues getting started. I was following the instructions for an anaconda installation in the readme file, but ran into this problem when installing nextflow. I've copied my terminal text below. I also tried using the package directly through command line but ran into a couple errors I think were due to bad install. Sorry if this isn't very helpful, I'm not much of a programmer....
(timsconcert) PS C:\Users\Lab Admin> conda install -c bioconda nextflow
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package zlib conflicts for:
nextflow -> curl[version='>=7.76.1,<8.0a0'] -> zlib[version='>=1.2.11,<1.3.0a0']
python=3.7 -> sqlite[version='>=3.33.0,<4.0a0'] -> zlib[version='>=1.2.11,<1.3.0a0']

Package vs2015_runtime conflicts for:
python=3.7 -> vs2015_runtime[version='>=14.16.27012,<15.0a0']
python=3.7 -> vc[version='>=14.1,<15.0a0'] -> vs2015_runtime[version='>=14.0.25123,<15.0a0|>=14.0.25420|>=14.15.26706|>=14.27.29016|>=14.16.27012']

Package vc conflicts for:
python=3.7 -> openssl[version='>=1.1.1e,<1.1.2a'] -> vc=9
python=3.7 -> vc[version='14.*|>=14.1,<15.0a0']

[mwang87]

oh man sorry for the delay. Window/WSL, honestly I personally have not done too much testing on it. Perhaps it woudl be better to totally create a fully separate conda environment that is clean to install rather than building upon an existing base.

[dtabb73]

Whether I attempt to run timsconvert via the Anaconda prompt or directly via Python on the ordinary command line on my Windows 11 workstation, I get errors that there is "no module named 'timsconvert'." The complexity of installation required for sophisticated Python tools is often error-prone enough for me to decide not to use them.

[gtluu]

Hi @tjlundgren, apologies for the delayed response but did you have any luck with the conda environment setup? Since you are just running this on Windows, nextflow should not be necessary, and you can invoke TIMSCONVERT from the command line without it (see this section in the README).

[gtluu]

@dtabb73 apologies for the delayed response as well, and I'm sorry about the installation difficulty.

That error generally occurs if the use of symbolic links are not enabled while cloning the repo using Git (see see Step 6 here in the README.

I'm not sure if this has changed in newer versions of Git, but previously when installing Git on Windows, you would need to check the box labeled "Enable symbolic links" as seen in the image below.

Unfortunately, if that was not enabled, a reinstall of Git may be the easiest option to enable it, followed by cloning the TIMSCONVERT repo again.

[animesh]

i reinstalled git with symbolic link enable checked but still i am facing probably a similar issue running Docker image created in windows via cmd.exe

C:\Users\animeshs\timsconvert>git clone https://github.com/gtluu/timsconvert
Cloning into 'timsconvert'...
remote: Enumerating objects: 4472, done.
remote: Counting objects: 100% (504/504), done.
remote: Compressing objects: 100% (259/259), done.
remote: Total 4472 (delta 266), reused 260 (delta 245), pack-reused 3968
Receiving objects: 100% (4472/4472), 55.45 MiB | 20.13 MiB/s, done.
Resolving deltas: 100% (3042/3042), done.

C:\Users\animeshs\tims>cd timsconvert


C:\Users\animeshs\tims\timsconvert>docker build --no-cache .
[+] Building 52.1s (9/9) FINISHED                                                                                                                            docker:default
 => [internal] load build definition from Dockerfile                                                                                                                   0.0s
 => => transferring dockerfile: 167B                                                                                                                                   0.0s
 => [internal] load .dockerignore                                                                                                                                      0.1s
 => => transferring context: 225B                                                                                                                                      0.0s
 => [internal] load metadata for docker.io/library/python:3.11                                                                                                         0.6s
 => [1/4] FROM docker.io/library/python:3.11@sha256:a46ef4ef9f9d4fee62ad368f9526552a0a99e90882d246cdefe50d356e3a74dd                                                   0.0s
 => [internal] load build context                                                                                                                                      0.1s
 => => transferring context: 10.13kB                                                                                                                                   0.0s
 => CACHED [2/4] WORKDIR /app                                                                                                                                          0.0s
 => [3/4] COPY . /app                                                                                                                                                  0.2s
 => [4/4] RUN pip3 install -r requirements.txt                                                                                                                        45.2s
 => exporting to image                                                                                                                                                 5.8s
 => => exporting layers                                                                                                                                                5.7s
 => => writing image sha256:d634a399f727de32c68978a7587ba64a1814c609209e43cb822ff3e77547859b                                                                           0.0s

View build details: docker-desktop://dashboard/build/default/default/pw0517b0u7g7asnvnzk4kkpws

What's Next?
  View a summary of image vulnerabilities and recommendations → docker scout quickview

C:\Users\animeshs\tims\timsconvert>docker images
REPOSITORY                TAG       IMAGE ID       CREATED          SIZE
<none>                    <none>    d634a399f727   58 seconds ago   1.73GB

C:\Users\animeshs\tims\timsconvert>docker run --rm -it d634a399f727
Traceback (most recent call last):
  File "/app/bin/run.py", line 1, in <module>
    from timsconvert import *
ModuleNotFoundError: No module named 'timsconvert'

C:\Users\animeshs\tims\timsconvert>

[animesh]

just an update, it seems to have worked via WSL 👍🏽 so i have loaded up the created docker image to hub https://hub.docker.com/r/animesh1977/timsconvert which can be pulled via windows cmd.exe

C:\Users\animeshs\tims\timsconvert>docker pull animesh1977/timsconvert
Using default tag: latest
latest: Pulling from animesh1977/timsconvert
ca4e5d672725: Already exists
30b93c12a9c9: Already exists
10d643a5fa82: Already exists
d6dc1019d793: Already exists
3f97c2dcac68: Already exists
10b660d66aed: Already exists
3c06c666a70d: Already exists
28fd036baf97: Already exists
b104391053fe: Pull complete
ca597157fd8c: Pull complete
5ea2a63cbfb5: Pull complete
Digest: sha256:acb1c9db5702c0e4bed4b437fd6c931407159925604920cada437578dce5dc48
Status: Downloaded newer image for animesh1977/timsconvert:latest
docker.io/animesh1977/timsconvert:latest

What's Next?
  View a summary of image vulnerabilities and recommendations → docker scout quickview animesh1977/timsconvert

and it seems to be running just fine 🤞

C:\Users\animeshs\tims\timsconvert>docker run --rm -it  -v C:\Users\animeshs\HeLaDIA:/data animesh1977/timsconvert --verbose --chunk_size 1000000 --input /data
2024-07-28T15:49:08.800351:Initialize Bruker .dll file...
2024-07-28T15:49:08.808132:Loading input data...
2024-07-28T15:49:22.210892:Reading file: /data/231123_hela_dia1_Slot1-54_1_5739.d
...

[gtluu]

Thanks for the update. The Docker container was written with Linux/Ubuntu in mind, so it makes sense that it only works in WSL.