#336 PR version

336_Atropos/atropos.eb

@@ -6,26 +6,20 @@ version = '1.1.32'
 homepage = 'https://atropos.readthedocs.io'
 description = "Atropos is tool for specific, sensitive, and speedy trimming of NGS reads."
 
-toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchain = {'name': 'gompi', 'version': '2023a'}
 
 dependencies = [
     ('Python', '3.11.3'),
     ('Python-bundle-PyPI', '2023.06'),
-    # ('SciPy-bundle', '2023.07'), # only for versioneer
     ('tqdm', '4.66.1'),
     ('Pysam', '0.22.0'),
     ('pytest', '7.4.2'),
+    ('SRA-Toolkit', '3.0.10'),
 ]
 
 use_pip = True
 sanity_pip_check = True
 
-# srastream 0.1.3 requires xphyle, which is not installed. OK
-# khmer 2.1.1 requires bz2file, which is not installed. OK
-# khmer 2.1.1 requires screed, which is not installed. OK
-# xphyle 4.0.5 requires pokrok, which is not installed. OK
-# ModuleNotFoundError: No module named 'ngs'
-
 exts_list = [
     ('versioneer', '0.29', {
         'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'],
@@ -39,15 +33,15 @@ exts_list = [
     ('khmer', '2.1.1', {
         'checksums': ['a709606910bb8679bd8525e9d2bf6d1421996272e343b54cc18090feb2fdbe24'],
     }),
-    # ('pokrok', '0.2.0', {
-    #     'checksums': ['cfe7956602d8bbc142a07bcb259e0d1d939f96d7b074e00dceea3cb5e39244e8'],
-    # }),
-    # ('xphyle', '4.0.5', {
-    #     'checksums': ['b744723a3c88d81318c7291c32682b8715a046f70d0a1db729bda783fd5e08bd'],
-    # }),
-    # ('srastream', '0.1.3', {
-    #     'checksums': ['7f2cfd76ae988349ad5407a952cd4c133ae5dff7cf12c76072c53d82b50c2634'],
-    # }),
+    ('pokrok', '0.2.0', {
+        'checksums': ['cfe7956602d8bbc142a07bcb259e0d1d939f96d7b074e00dceea3cb5e39244e8'],
+    }),
+    ('xphyle', '4.0.5', {
+        'checksums': ['b744723a3c88d81318c7291c32682b8715a046f70d0a1db729bda783fd5e08bd'],
+    }),
+    ('srastream', '0.1.3', {
+        'checksums': ['7f2cfd76ae988349ad5407a952cd4c133ae5dff7cf12c76072c53d82b50c2634'],
+    }),
     (name, version, {
         'checksums': ['17e9dc3d76d7a2ca607a12da191a6d7ba1cfbd1a8c924215870417f85858fd83'],
     }),
@@ -60,6 +54,4 @@ sanity_check_paths = {
 
 sanity_check_commands = ["atropos detect --help"]
 
-sanity_pip_check = True
-
 moduleclass = 'bio'