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rbloom5 / ImmuneRep

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Figure out structure of python path #8

Closed rbloom5 closed 9 years ago

rbloom5 commented 9 years ago

There are lots of packages that we need, and we will probably all put them in different locations. A simple way to make sure we don't have to input a bunch of paths every time would be a nice to have

rzeller commented 9 years ago

Probably a good thing to document in the wiki.

If someone is feeling ambitious, I think it would be best to have an installation script (setup.py) that sets up all the python dependencies.

ramanktalwar commented 9 years ago

Yeah, I really like the idea of an installation script. Maybe once we adda couple more scripts and it becomes unwielding I can figure out how to do that...

If you use pip to install packages it automatically puts them in site-directory, right? If we all did that, wouldn't we just be able to call it from import like anything else? Can you use pip on esoteric packages like VDJFasta? I haven't been able to get it to work....

rbloom5 commented 9 years ago

here is an explanation of how to use pip to get a package from github:

http://stackoverflow.com/questions/7322334/how-to-use-python-pip-install-software-to-pull-packages-from-github, not exactly what you are looking for, but close

also, it might be tricky calling in perl packages using python - not sure it will work the same - but i've never tried

On Tue, Dec 9, 2014 at 1:18 PM, ramanktalwar notifications@github.com wrote:

Yeah, I really like the idea of an installation script. Maybe once we adda couple more scripts and it becomes unwielding I can figure out how to do that...

If you use pip to install packages it automatically puts them in site-directory, right? If we all did that, wouldn't we just be able to call it from import like anything else? Can you use pip on esoteric packages like VDJFasta? I haven't been able to get it to work....

— Reply to this email directly or view it on GitHub https://github.com/rbloom5/ImmuneRep/issues/8#issuecomment-66359435.

ramanktalwar commented 9 years ago

Great point about VDJFasta and perl. I think you're exactly right.

For the other stuff, it would be nice if it was always installed properly in site-directory (things like SRA toolkit, AbMiner, etc.). But I don't think pip is finding those things. Does it only search a database of programs or can you point to things?

rzeller commented 9 years ago

We could write an installation script in bash. That might give us more flexibility.

We may also consider using git submodules. We could reference all the required packages from our main repo. That would also allow us to have our own versions of the packages.