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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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Fix version header when not in git #218

Closed brantfaircloth closed 3 years ago

brantfaircloth commented 3 years ago

Version is supposed to pull git hash when running from git and a version number when it's not (which is most people). However, currently displays:

 Version: 2.0_r_fatal: Not a git repository: '/home/bcf/conda/envs/phyluce-1.7/lib/python3.6/site-packages/.git'
warthmann commented 3 years ago

Hello, I am running a phyluce installed with conda. I am hence not in a git repo and I am getting a similar error: 

uce-tutorial$ phyluce_assembly_assemblo_trinity \
>     --conf assembly.conf \
>     --output trinity-assemblies \
>     --clean \
>     --cores 24
2021-03-03 17:28:19,182 - phyluce_assembly_assemblo_trinity - INFO - =========== Starting phyluce_assembly_assemblo_trinity ==========
2021-03-03 17:28:19,182 - phyluce_assembly_assemblo_trinity - INFO - Version: git fatal: Not a git repository: '/home/norman/data/miniconda3/envs/phyluce/lib/python2.7/site-packages/.git'
2021-03-03 17:28:19,182 - phyluce_assembly_assemblo_trinity - INFO - Argument --clean: True
2021-03-03 17:28:19,182 - phyluce_assembly_assemblo_trinity - INFO - Argument --config: /data/norman/coffee/allele_assembly/uce-tutorial/assembly.conf
2021-03-03 17:28:19,182 - phyluce_assembly_assemblo_trinity - INFO - Argument --cores: 8
2021-03-03 17:28:19,183 - phyluce_assembly_assemblo_trinity - INFO - Argument --dir: None
2021-03-03 17:28:19,183 - phyluce_assembly_assemblo_trinity - INFO - Argument --log_path: None
2021-03-03 17:28:19,183 - phyluce_assembly_assemblo_trinity - INFO - Argument --min_kmer_coverage: 2
2021-03-03 17:28:19,183 - phyluce_assembly_assemblo_trinity - INFO - Argument --output: /data/norman/coffee/allele_assembly/uce-tutorial/trinity-assemblies
2021-03-03 17:28:19,183 - phyluce_assembly_assemblo_trinity - INFO - Argument --subfolder: 
2021-03-03 17:28:19,183 - phyluce_assembly_assemblo_trinity - INFO - Argument --verbosity: INFO
2021-03-03 17:28:19,183 - phyluce_assembly_assemblo_trinity - INFO - Getting input filenames and creating output directories
brantfaircloth commented 3 years ago

Hi.

These are actually two slightly separate errors (the one I was dealing with is in an upgraded version of phyluce that's not yet released). It does not seem like your error is causing phyluce to stop working (if it is, a solution is to install git). The overall error should be fixed in the updated version I hope to release in a few days.

warthmann commented 3 years ago

however, more significant is this IOError: (seems some hard coded path somewhere)

2021-03-03 17:28:19,183 - phyluce_assembly_assemblo_trinity - INFO - Getting input filenames and creating output directories
Traceback (most recent call last):
  File "/home/norman/data/miniconda3/envs/phyluce/bin/phyluce_assembly_assemblo_trinity", line 362, in <module>
    main()
  File "/home/norman/data/miniconda3/envs/phyluce/bin/phyluce_assembly_assemblo_trinity", line 307, in main
    input = get_input_data(args.config, args.dir)
  File "/home/norman/data/miniconda3/envs/phyluce/lib/python2.7/site-packages/phyluce/raw_reads.py", line 142, in get_input_data
    raise IOError("{} is not a directory".format(sample[1]))
IOError: /scratch/bfaircloth-uce-tutorial/clean-fastq/alligator_mississippiensis/split-adapter-quality-trimmed is not a directory
brantfaircloth commented 3 years ago

It seems like the config file you're using to assemble includes paths on my computer to the data when these need to be paths on your computer to the data (e.g. the path to where you downloaded the data).

warthmann commented 3 years ago

I am also noting a copy/paste/edit glitch in the tutorial, https://phyluce.readthedocs.io/en/latest/tutorial-one.html# where I am supposed to substitute "phyluce_assembly_assemblo_trinity" for "phyluce_assembly_assemblo_trinity"

Trinity is no longer supported on MacOS (generally, or in phyluce), so substitute phyluce_assembly_assemblo_trinity for phyluce_assembly_assemblo_trinity.
brantfaircloth commented 3 years ago

Yep, also fixed in the update. phyluce_assembly_assemblo_spades will do what you need.

warthmann commented 3 years ago

indeed my bad, fixed now and running. Thanks for this speedy response!

brantfaircloth commented 3 years ago

you bet 👍. thanks for noting these!