Remove packaged btllib, make it a dependency (#90)

* Remove packaged btllib, make it a dependency

* Update README.md

Author: lcoombe

README.md

@@ -122,22 +122,21 @@ ntJoin assemble target=my_scaffolds.fa target_weight=1 reference_config=config_f
 * As of version 1.1.0, ntJoin can detect and trim overlaps between joined sequences. This feature is controlled by the `overlap` parameter, and is on `overlap=True` by default. To turn this behaviour off, specify `overlap=False`
 
 ## Installation Instructions
-#### Installing ntJoin using Brew
-ntJoin can be installed using [Homebrew](https://brew.sh) on macOS or [Linuxbrew](http://linuxbrew.sh) on Linux:
+
+#### Installing ntJoin using Conda
 ```sh
-brew install brewsci/bio/ntjoin
+conda install -c bioconda -c conda-forge ntjoin=1.1.0
 ```
 
-#### Installing ntJoin using Conda
+#### Installing ntJoin using Brew
+ntJoin can be installed using [Homebrew](https://brew.sh) on macOS or [Linuxbrew](http://linuxbrew.sh) on Linux:
 ```sh
-conda install -c bioconda -c conda-forge ntjoin=1.0.8
+brew install brewsci/bio/ntjoin
 ```
 
 #### Installing ntJoin from the source code
 ```sh
-git clone https://github.com/bcgsc/ntJoin.git
-cd ntJoin/src
-make
+curl -L --output ntJoin-1.1.0.tar.gz https://github.com/bcgsc/ntJoin/releases/download/v1.1.0/ntJoin-1.1.0.tar.gz && tar xvzf ntJoin-1.1.0.tar.gz 
 ```
 
 ## Dependencies
@@ -146,6 +145,7 @@ make
 * [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)
 
 Python dependencies can be installed with:
 ```sh

azure-pipelines.yml

@@ -30,10 +30,6 @@ jobs:
       pylint ntjoin_assemble.py read_fasta.py ntjoin_utils.py
       cd ..
     displayName: Run pylint
-  - script: make -C src all
-    displayName: Compile C++ executables
-  - script: make -C src check
-    displayName: Test C++ executables
   - script: |
       source activate ntjoin_CI
       conda install --yes --quiet --name ntjoin_CI -c conda-forge -c bioconda pytest bedtools samtools
@@ -45,7 +41,20 @@ jobs:
   pool:
     vmImage: macOS-latest
   steps:
-  - script: make -C src all
-    displayName: Compile C++ executables with clang
-  - script: make -C src check
-    displayName: Test C++ executables
+  - script: echo "##vso[task.prependpath]$CONDA/bin"
+    displayName: Add conda to PATH
+
+  - script: conda create --yes --quiet --name ntjoin_CI
+    displayName: Create Anaconda environment
+
+  - script: |
+      source activate ntjoin_CI
+      conda install --yes --quiet --name ntjoin_CI -c conda-forge -c bioconda python=3.9 pylint samtools=1.14
+      conda install --yes --quiet --name ntjoin_CI -c conda-forge -c bioconda --file requirements.txt
+    displayName: Install Anaconda packages
+  - script: |
+      source activate ntjoin_CI
+      conda install --yes --quiet --name ntjoin_CI -c conda-forge -c bioconda pytest bedtools samtools
+      cd tests
+      pytest -vs ntjoin_test.py
+    displayName: Run pytests

ntJoin

@@ -112,8 +112,6 @@ else
 gzip=gzip -f
 endif
 
-# Set-up PYTHON PATH
-PYTHONPATH=$(assemble_path)/src/btllib/install/lib/btllib/python
 
 help:
 	@echo ""
@@ -189,12 +187,20 @@ version:
 	@echo "ntJoin v1.1.0"
 	@echo "Written by Lauren Coombe (lcoombe@bcgsc.ca)"
 
-.PHONY: help all version analysis assemble check_params jupiter
+check_install:
+ifeq ($(shell command -v indexlr),)
+        $(error ERROR: indexlr not found. Please ensure btllib is installed)
+endif
+ifneq ($(shell command -v 'python3 -c "import btllib"'),)
+        $(error ERROR: btllib not found. Please ensure btllib is installed)
+endif
+
+.PHONY: help all version analysis assemble check_params jupiter check_install
 .DELETE_ON_ERROR: $(prefix).n$(n).mx.dot
 .SECONDARY:
 
 %.k$(k).w$(w).tsv: %
-	$(log_time) $(assemble_path)/src/indexlr --long --pos -k $(k) -w $(w) -t $(t) $< > $@
+	$(log_time) indexlr --long --pos -k $(k) -w $(w) -t $(t) $< > $@
 
 %.fai: %
 	$(log_time) samtools faidx $<
@@ -218,7 +224,7 @@ ifeq ($(overlap), True)
 endif
 
 $(target).k$(k).w$(w).n$(n).assigned.scaffolds.fa: $(target).k$(k).w$(w).tsv $(min_ref_targets)
-	PYTHONPATH=$(PYTHONPATH) $(log_time)  $(assemble_path)/bin/ntjoin_assemble.py -p $(prefix) -n $(n) -s $< -l $(target_weight) \
+	$(log_time)  $(assemble_path)/bin/ntjoin_assemble.py -p $(prefix) -n $(n) -s $< -l $(target_weight) \
 	-r "$(reference_weights_list)" -k $(k) -g $(g) -G $(G) -t $(assemble_t) $(ntjoin_assembly_opts) $(min_ref_targets)
 
 $(target).k$(k).w$(w).n$(n).unassigned.scaffolds.fa: $(target).k$(k).w$(w).n$(n).assigned.scaffolds.fa

requirements.txt

@@ -1,3 +1,4 @@
 python-igraph
 pybedtools
-pymannkendall
+pymannkendall
+btllib