Update - Patches for third party links used by Ariba

recipes/ariba/meta.yaml

@@ -8,9 +8,12 @@ package:
 source:
   url: https://pypi.io/packages/source/a/ariba/ariba-{{ version }}.tar.gz
   sha256: '{{ sha256 }}'
-
+  patches:
+    - pubmlst_getter.patch
+    - ref_genes_getter.patch  
+
 build:
-  number: 1
+  number: 2
   skip: True  # [py2k]
   script: python -m pip install --no-deps --ignore-installed .
 
@@ -30,7 +33,7 @@ requirements:
     - pyfastaq >=3.12.0
     - pysam >=0.15.3 # older versions have wrong openssl pinning
     - pymummer <=0.10.3
-    - bowtie2 >=2.3.1
+    - bowtie2 <2.4.0 
     - cd-hit >=4.6.5
     - samtools >=1.2
     - bcftools >=1.2
@@ -43,6 +46,8 @@ test:
   imports:
     - ariba
     - ariba.tasks
+  commands:
+    - "ariba version"
 
 about:
   home: https://github.com/sanger-pathogens/ariba

recipes/ariba/pubmlst_getter.patch

@@ -0,0 +1,23 @@
+From 6f0fb988cbc3d1f5386fd4ee67a73fae8005fb34 Mon Sep 17 00:00:00 2001
+From: "Robert A. Petit III" <[email protected]>
+Date: Mon, 17 Aug 2020 17:32:11 -0400
+Subject: [PATCH] Fix for changes in PubMLST url
+
+Related to https://github.com/sanger-pathogens/ariba/issues/304
+---
+ ariba/pubmlst_getter.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/ariba/pubmlst_getter.py b/ariba/pubmlst_getter.py
+index 444f88e..b46b7d8 100644
+--- a/ariba/pubmlst_getter.py
++++ b/ariba/pubmlst_getter.py
+@@ -105,7 +105,7 @@ def _download_profile_and_fastas(self, outdir, profile_url, fasta_urls):
+         self._download_file(profile_url, profile_outfile)
+
+         for fasta_url in fasta_urls:
+-            outfile = os.path.join(outdir, fasta_url.split('/')[-1])
++            outfile = "{0}.tfa".format(os.path.join(outdir, fasta_url.split('/')[-2]))
+             self._download_file(fasta_url, outfile + '.tmp')
+             PubmlstGetter._rename_seqs_in_fasta(outfile + '.tmp', outfile)
+             os.unlink(outfile + '.tmp')

recipes/ariba/ref_genes_getter.patch

@@ -0,0 +1,22 @@
+From 8a68981d04eb22ad2ab0fbd0e3fc48d7e8012163 Mon Sep 17 00:00:00 2001
+From: "Robert A. Petit III" <[email protected]>
+Date: Wed, 12 Aug 2020 14:29:52 -0400
+Subject: [PATCH] Solution 2 for fixing CARD downloads with getref
+
+---
+ ariba/ref_genes_getter.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/ariba/ref_genes_getter.py b/ariba/ref_genes_getter.py
+index 0279d71..8c7b9f0 100644
+--- a/ariba/ref_genes_getter.py
++++ b/ariba/ref_genes_getter.py
+@@ -42,7 +42,7 @@ def __init__(self, ref_db, version=None, debug=False):
+     def _get_card_versions(self, tmp_file):
+         print('Getting available CARD versions')
+         common.download_file('https://card.mcmaster.ca/download', tmp_file, max_attempts=self.max_download_attempts, sleep_time=self.sleep_time, verbose=True)
+-        p = re.compile(r'''href="(/download/.*?broad.*?v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.(gz|bz2))"''')
++        p = re.compile(r'''href="(/download/.*?broadstreet.*?v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.(gz|bz2))"''')
+         versions = {}
+
+         with open(tmp_file) as f: