SalmonTE on Galaxy server

[sarah872]

Does anyone know if it is already available through a publicGalaxy server?

[hyunhwan-jeong]

Hi @sarah872,

Thank you for your interested SalmonTE. I have not had any experience making any pipeline of mine available through a publicGalaxy server, but I believe it must be great to put this tool on the server. I will make a future plan on it, but I have to ask your patients to do it. I will be glad to any further suggestion or be providing any useful materials to help the implementation.

If you want to run SalmonTE right now and have any problem, then please do not hesitate to ask any question. I will glad to assist you.

Best,

Hyun-Hwan Jeong

[sarah872]

I am asking because (1) you reported problems when running on MacOS and (2) I could run it in a cluster, but for that the admin needs to install it

keep me updated! thanks

EDIT: when try to run SalmonTE.py, the decopt module isn't found although it is installed through 'pip3 install docopt'

[hyunhwan-jeong]

I will start work to solve the issue of MacOS with docker and will give an update in this week even it has not been finished.

For the pip3 issue, I believe pip3 must find the package, would you try below command?

pip3 install git+https://github.com/docopt/docopt --user

Best,

Hyun-Hwan Jeong

[sarah872]

getting the following when trying your command: Requirement already satisfied (use --upgrade to upgrade): docopt==0.6.2 from git+https://github.com/docopt/docopt in /Users/Tobias/Library/Python/3.6/lib/python/site-packages

[hyunhwan-jeong]

@sarah872,

The message shows the package has been installed. Are you having any problem and seeing any error message when you run salmonTE?

Thank you,

Hyun-Hwan Jeong

[hyunhwan-jeong]

Hi @sarah872,

I also have another thought for how to run it in your computing environment:

1. As we know, running it onmacOS may have a problem and I am still figuring out, so it will take the time to solve the issue. Are you trying to install it on your macOS machine now? I guess multiple obstacles will wait for you to run, so I would not recommend you to take this option now.

2. However, if you have a Linux machine and python3 is installed (I guess the OS is installed the cluster, so you are in the case), then SalmonTE can be installed with your account (i.e. without root or admin account), and you can use this pipeline in the machine.

Thank you,

Hyun-Hwan Jeong

[sarah872]

I will wait then as I don't have permissions to install packages keep me posted!

[hyunhwan-jeong]

Dear @sarah872,

I figured out the macOS problem was because snakemake which I used in one of my machine was outdated. The problem is resolved with upgrading the snakemake package, and you can try it. Please let me know if you have any problem, and I will open another issue for the macOS to explore your issue.

For the version public galaxy server, it would be difficult to implement it, so I am seeing another way to ease installation of the tool. I believe using docker must be the answer, and I will start the implementation soon. Please note me you are fine with the option, and I will close this issue once I got the answer from you.

Best Regards,

Hyun-Hwan Jeong

[sarah872]

Dear @hyunhwaj I am still getting the error:

dos13:SalmonTE Sarah$ python3 SalmonTE.py 

Traceback (most recent call last):
  File "SalmonTE.py", line 14, in <module>
    from docopt import docopt
ImportError: No module named 'docopt'

[hyunhwan-jeong]

@sarah872 Could you write down the problem #2 after now?

By the way, I guess you have multiple version of python3 now. Could you provide output of pip3 --version and python3 --version for the clarification fo the problem? Moreover, I would you ask to run following commands.

git clone https://github.com/docopt/docopt
cd docopt
python3 setup.py install

Thank you,

Hyun-Hwan Jeong