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sidhomj / DeepTCR

Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data
https://sidhomj.github.io/DeepTCR/
MIT License
113 stars 40 forks source link

Add Pillow to requirements #21

Closed choosehappy closed 4 years ago

choosehappy commented 4 years ago

Otherwise one receives an error saying TIF not supported when making heatmaps:

image

sidhomj commented 4 years ago

you mean add pillow as an import?

choosehappy commented 4 years ago

in the requirements.txt should do it?

i didn't modify your code, but received that error then did a "pip install pillow" then reran the same code and the error disappeared

i suspect it may be an "optional" dependency for the other libraries so isn't it automatically installed when doing pip install -r requirements.txt

On Sat, Nov 16, 2019 at 2:01 PM John-William Sidhom < notifications@github.com> wrote:

you mean add pillow as an import?

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sidhomj commented 4 years ago

got it

sidhomj commented 4 years ago

updated requirements.txt file. Now when you install, pip should also install all dependencies as well except for PhenoGraph which needs to be installed separately.

choosehappy commented 4 years ago

actually, you can add:

git+https://github.com/jacoblevine/phenograph.git

to the requirements.txt list and it will install it as well

btw, currently on line 19:

https://github.com/sidhomj/DeepTCR/blob/becc96bf709fdbac6cf8a634a33e21aedf32839d/requirements.txt#L19

there is an effort to load phenograph, which ends up causing an error:

  Could not find a version that satisfies the requirement PhenoGraph==1.5.2 (from -r requirements.txt (line 19)) (from versions: )
No matching distribution found for PhenoGraph==1.5.2 (from -r requirements.txt (line 19))
sidhomj commented 4 years ago

so it turns out when running the setup.py file, it can only install packages on pypi. I'm having difficulty getting the setup.py file to install phenograph with that command in the requirements.txt file