conda installation instructions don't work

[mw55309]

Not sure the last time you checked these, but the conda installation instructions don't work (certainly not on a raw ubuntu EC2 instance)

The pysam installation step errors out with "pysam is not in list", and if you remove the dependencies flag, it runs but errors with a load of conflicts.

The pip install instructions also error out with a missing package.

Could we get some updated installation instructions? :D

[angelovaag]

I get the same issue, completely

[angelovaag]

In an earlier issue a user suggested using "pip install pysam --user" to install pysam. that worked for me

[zekepuli]

pip install pysam --user

That worked for me too. Thanks!

[mw55309]

I always think if the answer is "pip" then you don't understand the question

pip install instructions also error out with a missing package.

[DRL]

Hi all,

I updated the instructions. Reopen if issues persist.

Good luck.

dom

[zekepuli]

Hi all,

I updated the instructions. Reopen if issues persist.

Good luck.

dom

I have this error when I use the new instalation method and run ./blobtools create:

Traceback (most recent call last):
  File "../blob_analysis/../blobtools/blobtools", line 4, in <module>
    from lib.interface import main
  File "../blobtools/lib/interface.py", line 44, in <module>
    from docopt import docopt, DocoptExit
ModuleNotFoundError: No module named 'docopt'

[DRL]

do you have the conda environment activated?

[zekepuli]

do you have the conda environment activated?

Yes, my steps were:

1. conda create -n blobtools
   conda activate blobtools
   conda install -c anaconda matplotlib docopt tqdm wget pyyaml git pysam

2. Run example of ./blobtools create

[DRL]

can you copy all the output of conda and blobtools into a file and post that?

[zekepuli]

can you copy all the output of conda and blobtools into a file and post that?

blob_install.txt

Here's the output. I fixed the installation because you're trying to install pysam using the anaconda channel. But after fixing that, the docopt package is not recognized anyway

[DRL]

could it be that you created a python2 environment?

[zekepuli]

It seems that I have both Python 2.7.18 and Python 3.12.3 in the environment. I don't remember if it was the docopt or the pysam package that requires Python=2.7* to be installed in order to work the blobtools create

[DRL]

None of them should require python2 ... i'd recommend you delete that environment and start again from scratch