mv io tmp
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hey @mgoubran ! Could you give me detail to why you rename "io" to "tmp" and then back? This bit:
( from inside [miracl dir] : where you placed the pipeline )
mv io tmp
pip install -e .
mv tmp io
do you mean move it to /tmp? Is the goal to run the pip command without including it?
yea exactly.. the pip install gives an error for some reason because of the 'io' folder (it's name) .. it was just a lazy fix for now
ah, I think it's because "io" is a pretty active standard module:
https://docs.python.org/2/library/io.html
What we can do is move the modules under the main module folder, and then likely there won't be conflict. I'll see what I can do and include in the PR.
I'm about to close up working for this evening, but I'm well along into getting this written up / tweaked and will definitely have something sometime tomorrow. I'll ping you!
hey @mgoubran ! Quick question - where did you get these atlases from?
ENV allen10="${MIRACL_HOME}/atlases/ara/template/average_template_10um.nii.gz"
ENV allen25="${MIRACL_HOME}/atlases/ara/template/average_template_25um.nii.gz"
ENV allen50="${MIRACL_HOME}/atlases/ara/template/average_template_50um.nii.gz"
We'd want a programmatic way to download and provide them in the container.
hey @vsoch .. there are originally downloaded from the Allen brain institute websites, but these versions are processed and converted .. these versions are included in the atlases folder in the google drive I shared with you .. so I guess we can download them from there or host them somewhere else
oh! I totally forgot to look there, derp :P. I'll try adding them to the repo / somewhere else we can download from.
lol no worries.. some of the files might be too large for the repo (I think the limit is 100 Mb / file) .. btw the other folder depends has two compiled dependencies .. those also prob have large files
I just built those from scratch, so I won't need those files unless they are different. Do you have some other place we can host that has a download link?
Yes, if you want to put them in box when the links are ready I can add.
I'm still testing the images, but I'll push to my branch now so you can see the changes. I don't know the details of how this is supposed to work, but it has a lot of complicated dependencies that have made it challenging! If there are functions that are available via other tools (eg, I can't put matlab in the container) those might be better if you intend for others to use it.