Unable to run ./test-installation.sh on M1 Mac

[Mercilena]

Python, bpipe-utils not found while running test installation.

(clinker) Mercilenas-MacBook-Pro:test mercilena$ ./test-installation.sh
/opt/anaconda3/envs/clinker/bin/bpipe: line 375: python: command not found
/opt/anaconda3/envs/clinker/bin/bpipe: line 413: ./../bin/bpipe-utils.sh: No such file or directory
Error: Could not find or load main class bpipe.Tail9
Caused by: java.lang.ClassNotFoundException: bpipe.Tail9
/opt/anaconda3/envs/clinker/bin/bpipe: line 819: killtree: command not found
(clinker) Mercilenas-MacBook-Pro:test mercilena$ 

Please suggest. Bpipe was successfully installed along with all the dependencies acording to the manual.

[breons]

Hi,

What version of bpipe are you using? Also, with the clinker environment enabled, can you run python without the error?

[Mercilena]

bpipe-0.9.11.
python cannot be found when running inside clinker environment .

[breons]

That is odd regarding the lack of python. Did you install the environment with conda create --name clinker python=2.7 anaconda? You can try to conda install python=2.7 but sometimes I find starting with a new environment causes less headaches.

In terms of bpipe, not exactly sure what's going on there, but v0.9.9.7 (http://download.bpipe.org/versions/bpipe-0.9.9.7.tar.gz) should be supported.

[Mercilena]

Thanks! Now, the python works inside clinker env.
(clinker) Mercilenas-MacBook-Pro:~ mercilena$ python --version
Python 3.9.16

While cloning clinker source code, should I clone it inside clinker env?

[Mercilena]

I deleted the old clinker env and made a new one. Now all the dependencies are installed and working.
While cloning clinker source code, should I clone it inside clinker env or deactivate the clinker env and then clone it?

[breons]

That's great! I will say that Clinker only supports python 2 (2.7 is fine as posted above). Python 3 will likely throw some syntax errors when you do get the pipeline running.

You can clone it with the environment activated or not, shouldn't make a difference.

If you're still having issues with bpipe, unpack that link I posted above somewhere accessible, navigate to the bin directory within the unpacked folder, and then add that to your path export PATH=$PATH:$PWD. That should get that working for you.

[Mercilena]

when I am trying to make clinker using python 2.7, i get this error:
(base) Mercilenas-MacBook-Pro:~ mercilena$ conda create --name clinker python=2.7 anaconda
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): failed

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/bioconda/noarch/repodata.json
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
'https//conda.anaconda.org/bioconda/noarch

[Mercilena]

How do I Test installation
To test whether everything is working as it should I run the below steps:

(clinker) Mercilenas-MacBook-Pro:Software_Library mercilena$ git clone https://github.com/Oshlack/Clinker.git
Cloning into 'Clinker'...
remote: Enumerating objects: 362, done.
remote: Counting objects: 100% (40/40), done.
remote: Compressing objects: 100% (35/35), done.
remote: Total 362 (delta 16), reused 19 (delta 5), pack-reused 322
Receiving objects: 100% (362/362), 56.44 MiB | 17.79 MiB/s, done.
Resolving deltas: 100% (190/190), done.
(clinker) Mercilenas-MacBook-Pro:Software_Library mercilena$ export CLINKERDIR=$PWD
(clinker) Mercilenas-MacBook-Pro:Software_Library mercilena$ which CLINKERDIR

there is no CLINKERDIR. Please guide.

[breons]

You'll need the $ for an environment variable, i.e. $CLINKERDIR will show the directory you just exported to that variable.

Then it should just be a matter of following along this section of the installation documentation and beyond (the under the hood section will show you how to run it on your samples).

I.e.

1. Do a cd $CLINKERDIR/test
2. then ./test-installation.sh

Where $CLINKERDIR is the location you set above

after the pipeline finishes a new plot should appear in $CLINKERDIR/test/results/plots/test/BCR_ABL1.pdf

I hope that helps.

[breons]

Also, when you're ready to run your samples, you pretty much just want to create the below command (modifying the paths and parameters below as outlined in the wiki to suit you):

bpipe -p out="/path/to/clinker/output" -p caller="/path/to/jaffa_results.csv" -p col="3,4,5,6" -p del="c" -p genome="19" -p print="true" -p fusions="BCR:ABL1" -p pdf_width="9" -p pdf_height="16" -p sizing="1,3,1,2,4,2" -p competitive="true" $CLINKERDIR/workflow/clinker.pipe /path/to/*.fastq.gz