Prepare for release v1.1.2

.gitignore

@@ -0,0 +1,10 @@
+tests/*dot
+tests/*path
+tests/*agp
+tests/*fai
+tests/*assigned*fa
+tests/*all*fa
+tests/*tsv
+tests/*bed
+tests/*time
+*tar.gz

README.md

@@ -125,7 +125,7 @@ ntJoin assemble target=my_scaffolds.fa target_weight=1 reference_config=config_f
 
 #### Installing ntJoin using Conda
 ```sh
-conda install -c bioconda -c conda-forge ntjoin=1.1.1
+conda install -c bioconda -c conda-forge ntjoin=1.1.2
 ```
 
 #### Installing ntJoin using Brew
@@ -136,7 +136,7 @@ brew install brewsci/bio/ntjoin
 
 #### Installing ntJoin from the source code
 ```sh
-curl -L --output ntJoin-1.1.1.tar.gz https://github.com/bcgsc/ntJoin/releases/download/v1.1.1/ntJoin-1.1.1.tar.gz && tar xvzf ntJoin-1.1.1.tar.gz 
+curl -L --output ntJoin-1.1.2.tar.gz https://github.com/bcgsc/ntJoin/releases/download/v1.1.2/ntJoin-1.1.2.tar.gz && tar xvzf ntJoin-1.1.2.tar.gz 
 ```
 
 ## Dependencies
@@ -145,7 +145,7 @@ curl -L --output ntJoin-1.1.1.tar.gz https://github.com/bcgsc/ntJoin/releases/do
 * [bedtools v2.29.2+](https://bedtools.readthedocs.io/en/latest/)
 * [samtools](https://github.com/samtools/samtools)
 * [zlib](https://www.zlib.net/)
-* [btllib](https://github.com/bcgsc/btllib) v1.4.10 or lower
+* [btllib](https://github.com/bcgsc/btllib)
 
 Python dependencies can be installed with:
 ```sh

bin/ntjoin_assemble.py

@@ -981,7 +981,7 @@ def parse_arguments():
                                        "increasing/decreasing to assign contig orientation [90]\n "
                                        "Note: Only used with --mkt is NOT specified", default=90, type=int)
         parser.add_argument('-t', help="Number of threads for multiprocessing [1]", default=1, type=int)
-        parser.add_argument("-v", "--version", action='version', version='ntJoin v1.1.1')
+        parser.add_argument("-v", "--version", action='version', version='ntJoin v1.1.2')
         parser.add_argument("--agp", help="Output AGP file describing scaffolds", action="store_true")
         parser.add_argument("--no_cut", help="Do not cut input contigs, place in most representative path",
                             action="store_true")
@@ -1028,7 +1028,7 @@ def print_parameters(self):
 
     def main(self):
         "Run ntJoin graph stage"
-        print("Running ntJoin v1.1.1 ...\n")
+        print("Running ntJoin v1.1.2 ...\n")
         self.print_parameters()
 
         # Parse the weights of each input reference assembly

ntJoin

@@ -2,7 +2,7 @@
 
 # ntJoin: Scaffold assemblies using reference assemblies and minimizer graphs
 # Written by Lauren Coombe @lcoombe
-# ntJoin v1.1.1
+# ntJoin v1.1.2
 
 # Input files
 target=None
@@ -116,7 +116,7 @@ endif
 help:
 	@echo ""
 	@echo "ntJoin: Scaffolding assemblies using reference assemblies and minimizer graphs"
-	@echo "ntJoin v1.1.1"
+	@echo "ntJoin v1.1.2"
 	@echo "Usage: ntJoin assemble target=<target scaffolds> references='List of reference assemblies' reference_weights='List of weights per reference assembly'"
 	@echo ""
 	@echo "Options:"
@@ -184,7 +184,7 @@ ifeq ($(ref), None)
 endif
 
 version:
-	@echo "ntJoin v1.1.1"
+	@echo "ntJoin v1.1.2"
 	@echo "Written by Lauren Coombe (lcoombe@bcgsc.ca)"
 
 check_install:

requirements.txt

@@ -1,4 +1,4 @@
 python-igraph
 pybedtools
 pymannkendall
-btllib <=1.4.10
+btllib

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="ntJoin",
-    version="1.1.1",
+    version="1.1.2",
     author="Lauren Coombe",
     author_email="lcoombe@bcgsc.ca",
     description="Genome assembly scaffolder using minimizer graphs",