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greenelab / GCB535

Materials for GCB535 at Penn.
BSD 3-Clause "New" or "Revised" License
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Add Compute Environment Packages Here #155

Open gwaybio opened 6 years ago

gwaybio commented 6 years ago

We need to confirm that all of the packages and dependencies exist in the cocalc environment

We should explore specifying a custom conda environment https://github.com/sagemathinc/cocalc/wiki/Programming#anaconda-jupyter

Packages

gwaybio commented 6 years ago

We will test each module to see if the packages are available.

gwaybio commented 6 years ago

linked with #146 #147

gwaybio commented 6 years ago

The kernel workflow works! Please add packages (python, R, command line, etc.) and specific versions here

gwaybio commented 6 years ago

Also related to #122

gwaybio commented 6 years ago

Also related to #77

cgreene commented 6 years ago

samtools https://github.com/greenelab/GCB535/issues/92

cgreene commented 6 years ago

sklearn - i think that some of the ML exercises will break with the move to any recent version (that's ok). I had convert them last year to an older version b/c sagemath was running something quite old

I'd go with the current release (0.19) and we'll fix the exercises.

gwaybio commented 6 years ago

added HOMER 4.9.1

gwaybio commented 6 years ago

https://bioconda.github.io/recipes/phylip/README.html

:point_up: this is Phylip

cgreene commented 6 years ago

Just to make sure - are we sure we know how to distribute this to students as well? If there instructions they'll need to run, then we need to put them in the first exercise.

gwaybio commented 6 years ago

they're running everything in cocalc correct, not on their local machines? It should be automatically distributed in the notebooks. Command line interfaces outside of notebooks are trickier but we can do 1 of 2 things.

  1. setup aliases pointing to our versions.

e.g.

alias samtools='/home/user/.conda/envs/python-kernel-GCB535/bin/samtools'
  1. ask students to initialize environment every time they open a terminal
# in .bashrc
alias setenv='anaconda3 && source activate python-kernel-GCB535'
gwaybio commented 6 years ago

i guess I should confirm this a the student account. on it!

cgreene commented 6 years ago

I think that if you are asking students do so this every time then it is unlikely to occur. Things need to be as easy as opening a terminal (so we may need to add it to their bashrc files somehow). There may be a way to initially define a bashrc file that they inherit from.

gwaybio commented 6 years ago

bedtools

gwaybio commented 6 years ago

ugh... the kernels are NOT automatically transferred to the student users.

Unknown kernel python-kernel-GCB535 (select a valid kernel from the Kernel menu) FileEditViewInsertCellKernelHelp

Either we use the previous solution with built-in kernels and request packages when we need them or I dig deeper into figuring out how to transfer custom kernels to students (wasn't there a technical contact from cocalc for these kind of things?)

cgreene commented 6 years ago

Click the help button in the upper right to start a ticket. They're quick.

On Thu, Dec 21, 2017 at 3:50 PM Greg Way notifications@github.com wrote:

ugh... the kernels are NOT automatically transferred to the student users.

Unknown kernel python-kernel-GCB535 (select a valid kernel from the Kernel menu) FileEditViewInsertCellKernelHelp

Either we use the previous solution with built-in kernels and request packages when we need them or I dig deeper into figuring out how to transfer custom kernels to students (wasn't there a technical contact from cocalc for these kind of things?)

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gwaybio commented 6 years ago

Ticket submitted (ticket num: 4606)

  1. We are interested in creating custom jupyter kernels with conda environments. We have successfully created a custom Jupyter kernel using these instructions https://github.com/sagemathinc/cocalc/wiki/Programming#anaconda-jupyter.
  2. Our goal is to perpetuate this environment to students, but it seems this is not done automatically.
  3. Is there functionality to define a custom kernel, send to students, and be able to update between assignments? We have discussed this issue in some amount of detail here: https://github.com/greenelab/GCB535/issues/155
gwaybio commented 6 years ago

I moved this to the 2019 milestone, but we should add to this list throughout the 2018 semester