Compatibility issues between minos' gramtools.py script and gramtools' command

[ycode-sh]

I have not been able to successfully use minos as a result of errors associated with dependencies. Particularly, the options passed to gramtools when running "minos adjudicator" seems to be incorrect and often return an error. For example, the run_gramtools function in the minos/gramtools.py script specifies "quasimap" command. This is not recognized by gramtools and thus stops the run.

Already, I have spent several hours trying to detect and troubleshoot but still couldn't resolve the issues. Can anyone please help?

[iqbal-lab]

Hi there, can you explain how you installed minos? Version, method, etc?

[ycode-sh]

Thanks for your reply.
First, I cloned the git repository and then installed with pip3 install. Then I tried running minos with my data and the "new" test data provided provided but gramtools always returned error.
Second, I downloaded the tarball on the repository and installed according to instruction given but the problem persisted.
PS: All dependencies are installed.

[ycode-sh]

I installed minos version 0.12.4

[martinghunt]

Which version of gramtools did you install? Minos needs commit 8af53f6c8c0d72ef95223e89ab82119b717044f2 of gramtools.

[ycode-sh]

I installed gramtools version 1.10.0

[iqbal-lab]

That would explain your problem then, minos needs commit 8af53f6c8c0d72ef95223e89ab82119b717044f2

[ycode-sh]

Thanks a lot. I have searched through the ten versions of gramtools and their respective commits. None had 8af53f6c8c0d72ef95223e89ab82119b717044f2 commit. Please can you help me with how to find the specific commit?

[martinghunt]

git clone https://github.com/iqbal-lab-org/gramtools
cd gramtools
git checkout 8af53f6c8c0d72ef95223e89ab82119b717044f2

[ycode-sh]

Thank you so much. I started working on it immediately you sent the solution. Indeed I was able to checkout the hash code but afterwards ran into a series of new problems. First, gramtools couldn't install properly again. Second, I tried running "minos adjudicate" with some of my data and ran into an error that has to do with "vt normalize", even though vt has been properly installed. I then used the test data but got an error referring me to the "run_gramtools" function in the gramtools.py script. I've been on this for the past 5 hours now. Please help me out

[ycode-sh]

git clone https://github.com/iqbal-lab-org/gramtools
cd gramtools
git checkout 8af53f6c8c0d72ef95223e89ab82119b717044f2
After running the commands above, I ran the following;
bash ./gramtools/travis_build.sh
pip install ./gramtools

I am not sure I did the right thing.

[martinghunt]

I recommend using Singularity or Docker if possible, because it means you don't have to do any of this stuff.

That said, to install gramtools, this should work:

git clone https://github.com/iqbal-lab-org/gramtools
cd gramtools
git checkout 8af53f6c8c0d72ef95223e89ab82119b717044f2
pip3 install .

If the last command doesn't work, then this should work (it is what the singularity and docker builds do):

git clone https://github.com/iqbal-lab-org/gramtools
cd gramtools
git checkout 8af53f6c8c0d72ef95223e89ab82119b717044f2
mkdir cmake-build
cd cmake-build
cmake .. -DCMAKE_BUILD_TYPE=REL_WITH_ASSERTS
make gram
cd ..
pip3 install -e .

The commands used for the build are all in this file: https://github.com/iqbal-lab-org/minos/blob/master/.ci/install_dependencies.sh

[ycode-sh]

Thank you very much. I will try it out and if it doesn't work, I will use the docket container just as you suggested. Thanks a lot

[ycode-sh]

Eventually, minos worked perfectly on docker.
However, I'm using minos in a workflow that includes many other tools. To be sure the workflow works properly, I first have to test-run it locally, and thus need minos be installable locally too.
I have tried following the installation protocol using the code contained in
https://github.com/iqbal-lab-org/minos/blob/master/.ci/install_dependencies.sh
but failed. The challenge has been with installing gram tools ( during the py-cortex-api build stage) and this is really frustrating. @martinghunt and @iqbal-lab please assist me.

[ycode-sh]