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foerstner-lab / READemption

A pipeline for the computational evaluation of RNA-Seq data
https://reademption.readthedocs.io
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installation issue #24

Closed Haley-Wami closed 4 years ago

Haley-Wami commented 4 years ago

Hello,

I am trying to install (via pip) READemption and run into an error. I have all the requirements (Ubuntu packages, segemehl v0.2.0, DESeq2) installed and functional. However, running bin/reademption -h gives the following error.

Traceback (most recent call last): File "bin/reademption", line 6, in from reademptionlib.controller import Controller File "/home/haley/.local/lib/python3.5/site-packages/reademptionlib/controller.py", line 15, in from reademptionlib.readaligner import ReadAligner File "/home/haley/.local/lib/python3.5/site-packages/reademptionlib/readaligner.py", line 1, in from reademptionlib.segemehl import Segemehl File "/home/haley/.local/lib/python3.5/site-packages/reademptionlib/segemehl.py", line 68 tmp_sorted_outfile = f"{output_file}_sorted" ^ SyntaxError: invalid syntax

I downloaded the .tar.gz and run make also gives me the following issue. ERROR tests/test_controller.py ERROR tests/test_segemehl.py

I appreciate any help in advance!

Tillsa commented 4 years ago

Hello! Thank you for reporting the error. I assume the error occurs because you are using python version 3.5 which does NOT support f-strings. Line 68 is using an f-string. Could you please install a newer version that is at least 3.6, where f-strings have been introduced and then try again. And please let me know if it worked.

Best regards, Till

Haley-Wami commented 4 years ago

Hello Till,

That fixed the issue thanks a lot for your help!

Kind regards, Haley

Tillsa commented 4 years ago

You're welcome!