🐛 URL in ncbi-download-genome needed to be changed

vdclab · Mar 16, 2024 · bca7303 · bca7303
1 parent 18bb7ef
commit bca7303
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Showing 3 changed files with 11 additions and 11 deletions.
diff --git a/workflow/envs/biopython_ete3.yaml b/workflow/envs/biopython_ete3.yaml
@@ -5,5 +5,5 @@ dependencies:
   - pandas = 1.4.0
   - biopython = 1.79
   - ete3 = 3.1.2
-  - ncbi-genome-download = 0.3.0
-  - numpy = 1.21.5
+  - ncbi-genome-download = 0.3.3
+  - numpy = 1.21.6
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -1,4 +1,4 @@
-ngs.##########################################################################
+##########################################################################
 ##########################################################################
 ##
 ##                                Library

diff --git a/workflow/scripts/fetch_proteome.py b/workflow/scripts/fetch_proteome.py
@@ -1,15 +1,13 @@
-from distutils import cmd
+import shlex
+import os
+import sys
+import gzip
+import subprocess
 import pandas as pd
+import numpy as np
 from ete3 import NCBITaxa
-import os, sys
-import gzip
 from Bio import SeqIO
-from urllib.request import urlopen
-import subprocess
-import shlex
 import ncbi_genome_download as ngd
-import resource
-import numpy as np
 
 ##########################################################################
 
@@ -38,12 +36,14 @@ def get_cmdline_ndg(
                                       -l {assembly_levels} --flat-output\
                                       -o {output} -p {parallel}\
                                       -m {metadata_table} -R {refseq_categories}\
+                                      --uri https://ftp.ncbi.nlm.nih.gov/genomes\
                                       -t {','.join(taxids)} {groups}"
     else:
         cmd_line = f"python{python_version} {ncbi_genome_download} -s {section} -F {file_formats}\
                                       -l {assembly_levels}\
                                       -o {output} -p {parallel}\
                                       -m {metadata_table} -R {refseq_categories}\
+                                      --uri https://ftp.ncbi.nlm.nih.gov/genomes\
                                       -t {','.join(taxids)} {groups}"
 
     cmd_line = cmd_line.replace(" " * 37, "")