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| author | Pjotr Prins | 2020-12-31 10:51:57 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2020-12-31 10:51:57 +0000 |
| commit | c54c6624ce864daec7640d938a98f196fde4ba1e (patch) | |
| tree | 618047c0869630ffa2d86c4e4890e02266aa3173 /workflows/pull-data | |
| parent | e33ce088225b9975a84a6724ab8e3a9f82964ec6 (diff) | |
| download | bh20-seq-resource-c54c6624ce864daec7640d938a98f196fde4ba1e.tar.gz bh20-seq-resource-c54c6624ce864daec7640d938a98f196fde4ba1e.tar.lz bh20-seq-resource-c54c6624ce864daec7640d938a98f196fde4ba1e.zip | |
genbank: started on SPARQL fetcher
Diffstat (limited to 'workflows/pull-data')
| -rw-r--r-- | workflows/pull-data/genbank/.guix-run | 11 | ||||
| -rwxr-xr-x | workflows/pull-data/genbank/genbank-fetch-ids | 3 | ||||
| -rwxr-xr-x | workflows/pull-data/genbank/genbank-fetch-ids.py | 0 |
3 files changed, 10 insertions, 4 deletions
diff --git a/workflows/pull-data/genbank/.guix-run b/workflows/pull-data/genbank/.guix-run index 1403c69..6db7871 100644 --- a/workflows/pull-data/genbank/.guix-run +++ b/workflows/pull-data/genbank/.guix-run @@ -1,5 +1,8 @@ -#!/bin/sh -# Runner +# Set up the Guix environment with dependencies +# + +echo # next run: +echo 'export PATH=$GUIX_ENVIRONMENT/bin:$PATH' + +~/.config/guix/current/bin/guix environment guix --ad-hoc python python-biopython python-requests python-dateutil ruby -echo python3 from_genbank_to_fasta_and_yaml.py -guix environment guix --ad-hoc python python-biopython python-requests python-dateutil diff --git a/workflows/pull-data/genbank/genbank-fetch-ids b/workflows/pull-data/genbank/genbank-fetch-ids new file mode 100755 index 0000000..00f693f --- /dev/null +++ b/workflows/pull-data/genbank/genbank-fetch-ids @@ -0,0 +1,3 @@ +#!/usr/bin/env ruby +# +# diff --git a/workflows/pull-data/genbank/genbank-fetch-ids.py b/workflows/pull-data/genbank/genbank-fetch-ids.py deleted file mode 100755 index e69de29..0000000 --- a/workflows/pull-data/genbank/genbank-fetch-ids.py +++ /dev/null |