From 8412557f48165e613738c28460ea8aedcc97ae48 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Mon, 9 Dec 2024 16:24:44 +0100
Subject: [PATCH] #467 liqa ec + add gcmr to CRAN

---
 467_scNanoGPS/{Liqa.eb => liqa.eb} |  5 +++++
 467_scNanoGPS/scNanoGPS_v2.eb      | 19 ++++++++++---------
 2 files changed, 15 insertions(+), 9 deletions(-)
 rename 467_scNanoGPS/{Liqa.eb => liqa.eb} (86%)

diff --git a/467_scNanoGPS/Liqa.eb b/467_scNanoGPS/liqa.eb
similarity index 86%
rename from 467_scNanoGPS/Liqa.eb
rename to 467_scNanoGPS/liqa.eb
index 416b15b1..c7a5040f 100644
--- a/467_scNanoGPS/Liqa.eb
+++ b/467_scNanoGPS/liqa.eb
@@ -10,6 +10,9 @@ events using long-read RNA-seq data."""
 
 toolchain = {'name': 'gfbf', 'version': '2023a'}
 
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['f8b2e6f0226d99f513d17be3758e6b3e2e9b7b40579f840d28737e827358850e']
+
 # Liqa deps:
     # OK Python
         # OK Pysam
@@ -34,4 +37,6 @@ use_pip = True
 sanity_pip_check = True
 download_dep_fail = True
 
+sanity_check_commands = ['liqa -h']
+
 moduleclass = 'bio'
diff --git a/467_scNanoGPS/scNanoGPS_v2.eb b/467_scNanoGPS/scNanoGPS_v2.eb
index 7be3f1e3..5604de89 100644
--- a/467_scNanoGPS/scNanoGPS_v2.eb
+++ b/467_scNanoGPS/scNanoGPS_v2.eb
@@ -59,9 +59,10 @@ dependencies = [
     ('Longshot', '1.0.0'),
     ('BCFtools', '1.21'),
     ('gffread', '0.12.7'),
-    ('lifelines', '0.28.0'),
-    ('R', '4.3.2'),
-    ('R-bundle-CRAN', '2023.12'),
+    ('Liqa', '1.3.4'),
+    # ('lifelines', '0.28.0'),
+    # ('R', '4.3.2'),
+    # ('R-bundle-CRAN', '2023.12'),
     # annovar
 ]
 
@@ -74,22 +75,22 @@ exts_default_options = {
 }
 
 exts_list = [
-    ('liqa', '1.3.4', {
-        'modulename': False,
-        'checksums': ['f8b2e6f0226d99f513d17be3758e6b3e2e9b7b40579f840d28737e827358850e'],
-    }),
+    # ('liqa', '1.3.4', {
+    #     'modulename': False,
+    #     'checksums': ['f8b2e6f0226d99f513d17be3758e6b3e2e9b7b40579f840d28737e827358850e'],
+    # }),
     ('Distance', '0.1.3', {
         'checksums': ['60807584f5b6003f5c521aa73f39f51f631de3be5cccc5a1d67166fcbf0d4551'],
     }),
 ]
 
 sanity_check_paths = {
-    'files': ['bin/liqa'],
+    'files': [],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],
 }
 
 sanity_check_commands = [
-    "liqa -h",
+    'liqa -h',
     "python -c 'import distance'",
     "python other_utils/read_length_profiler.py -h",
     "python scanner.py -h",