search

hyunhwan-jeong / SalmonTE

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
GNU General Public License v3.0
81 stars 23 forks source link

SalmonTE example doesn't work #69

Closed sulevk closed 1 year ago

sulevk commented 2 years ago

Thank you for the salmonTE, great tool. However, running it is a bit cumbersome. After installation I tried to run example and got this: ./SalmonTE.py quant --reference=hs example 2022-06-19 12:39:55,355 Starting quantification mode 2022-06-19 12:39:55,356 Collecting FASTQ files... 2022-06-19 12:39:55,356 SalmonTE assumes that 'example' is a directory, and SalmonTE will search any FASTQ file in the directory. 2022-06-19 12:39:55,361 The input dataset is considered as a paired-ends dataset. 2022-06-19 12:39:55,362 Collected 4 FASTQ files. 2022-06-19 12:39:55,362 Quantification has been finished. 2022-06-19 12:39:55,362 Running Salmon using Snakemake Traceback (most recent call last): File "/Users/sulevkoks/Terminalis/SalmonTE/./SalmonTE.py", line 292, in run(args) File "/Users/sulevkoks/Terminalis/SalmonTE/./SalmonTE.py", line 243, in run run_salmon(param) File "/Users/sulevkoks/Terminalis/SalmonTE/./SalmonTE.py", line 143, in run_salmon snakemake.snakemake( AttributeError: module 'snakemake' has no attribute 'snakemake'

It is MACOS 12.4. Thank you for your comments.

hyunhwan-jeong commented 2 years ago

Duplicate of #70