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informative output if data not installed correctly
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aineniamh committed Jul 22, 2020
1 parent 336b1eb commit 9448578
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions pangolin/command.py
Original file line number Diff line number Diff line change
Expand Up @@ -188,7 +188,7 @@ def main(sysargs = sys.argv[1:]):


if representative_aln=="" or guide_tree=="" or lineages_csv=="":
print("""Check your environment, didn't find appropriate files from the lineages repo.\nTreefile must end with `.treefile`.\
print("""Check your environment, didn't find appropriate files from the lineages repo, please see https://cov-lineages.org/pangolin.html for installation instructions. \nTreefile must end with `.treefile`.\
\nAlignment must be in `.fasta` format.\n Trained model must exist. \
If you've specified --include-putative\n \
you must have files ending in putative.fasta.treefile\nExiting.""")
Expand Down Expand Up @@ -218,7 +218,7 @@ def main(sysargs = sys.argv[1:]):
elif fn.endswith(".csv") and fn.startswith("lineages"):
lineages_csv = os.path.join(r, fn)
if trained_model=="" or header_file=="" or lineages_csv=="":
print("""Check your environment, didn't find appropriate files from the pangoLEARN repo.\n Trained model must be installed.""")
print("""Check your environment, didn't find appropriate files from the pangoLEARN repo.\n Trained model must be installed, please see https://cov-lineages.org/pangolin.html for installation instructions.""")
exit(1)
else:
print("\nData files found")
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