Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
comparison amplicon_analysis_pipeline.py @ 11:570228bb2fb7 draft
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 53544cd620f81c5cfbdcb277e835f1c6da8588b0
| author | pjbriggs |
|---|---|
| date | Mon, 18 Jun 2018 07:27:33 -0400 |
| parents | b47cf1d6fb47 |
| children | fb2af52d67d1 |
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| 10:b47cf1d6fb47 | 11:570228bb2fb7 |
|---|---|
| 185 sys.stderr.write("Missing 'vsearch[113]'\n") | 185 sys.stderr.write("Missing 'vsearch[113]'\n") |
| 186 # Pipeline wants 'fasta-splitter.pl' but bioconda provides | 186 # Pipeline wants 'fasta-splitter.pl' but bioconda provides |
| 187 # 'fasta-splitter' | 187 # 'fasta-splitter' |
| 188 fasta_splitter = find_executable("fasta-splitter.pl") | 188 fasta_splitter = find_executable("fasta-splitter.pl") |
| 189 if fasta_splitter is None: | 189 if fasta_splitter is None: |
| 190 fasta_splitter = os.path.readlink( | 190 fasta_splitter = os.readlink( |
| 191 find_executable("fasta-splitter")) | 191 find_executable("fasta-splitter")) |
| 192 if fasta_splitter: | 192 if fasta_splitter: |
| 193 os.symlink(vsearch,os.path.join("bin","fasta-splitter.pl")) | 193 os.symlink(vsearch,os.path.join("bin","fasta-splitter.pl")) |
| 194 else: | 194 else: |
| 195 sys.stderr.write("Missing 'fasta-splitter[.pl]'\n") | 195 sys.stderr.write("Missing 'fasta-splitter[.pl]'\n") |