Remove packaged btllib, make a dependency (#56)

* Remove packaged btllib from ntLink, add packaged dependency

* Remove full path to indexlr

README.md

@@ -106,9 +106,7 @@ See the wiki page for more details.
 
  Installing from source code:
  ```
-git clone https://github.com/bcgsc/ntLink.git
-cd src
-make
+curl -L --output ntLink-1.3.1.tar.gz https://github.com/bcgsc/ntLink/releases/download/v1.3.1/ntLink-1.3.1.tar.gz && tar xvzf ntLink-1.3.1.tar.gz 
 ```
 
 #### Testing your installation
@@ -121,13 +119,14 @@ The expected output files can be found in: `tests/expected_outputs`
 
 ## Dependencies
 * Python 3.7+ ([Numpy](https://numpy.org/), [Python-igraph](https://igraph.org/python/))
+* [btllib](https://github.com/bcgsc/btllib)
 * [ABySS v2.3.0+](https://github.com/bcgsc/abyss)
 * GCC 6+ or Clang 5+ with OpenMP
 * [zlib](https://zlib.net/)
 
 Python dependencies can be installed with:
 ```
-pip3 install -r requirements.txt
+conda install -c bioconda --file requirements.txt
 ```
 
 ## License

azure-pipelines.yml

@@ -12,13 +12,6 @@ jobs:
 
   - script: conda create --yes --quiet --name ntlink_CI
     displayName: Create Anaconda environment
-
-  - script: |
-      curl https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add -
-      sudo apt-add-repository "deb http://apt.llvm.org/xenial/ llvm-toolchain-xenial-11 main"
-      sudo apt-get update
-      sudo apt-get install -y --no-install-recommends clang-format clang-tidy
-    displayName: Install clang-format and clang-tidy
   - script: |
       source activate ntlink_CI
       conda install --yes --quiet --name ntlink_CI -c conda-forge -c bioconda python pylint pytest pandas abyss=2.3.1
@@ -30,14 +23,6 @@ jobs:
       pylint ntlink_pair.py ntlink_utils.py ntlink_stitch_paths.py ntlink_overlap_sequences.py ntlink_filter_sequences.py
       cd ..
     displayName: Run pylint
-  - script: |
-      source activate ntlink_CI
-      make -C src all
-    displayName: Compile C++ executables
-  - script: |
-      source activate ntlink_CI
-      make -C src check
-    displayName: Test C++ executables
   - script: |
       source activate ntlink_CI
       cd tests
@@ -48,7 +33,17 @@ 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 ntlink_CI
+    displayName: Create Anaconda environment
+  - script: |
+      source activate ntlink_CI
+      conda install --yes --quiet --name ntlink_CI -c conda-forge -c bioconda python pylint pytest pandas abyss=2.3.1
+      conda install --yes --quiet --name ntlink_CI -c conda-forge -c bioconda --file requirements.txt
+    displayName: Install Anaconda packages
+  - script: |
+      source activate ntlink_CI
+      cd tests
+      pytest -vs ntlink_pytest.py
+    displayName: Run pytests

ntLink

@@ -92,9 +92,6 @@ else
 gzip=gzip -f
 endif
 
-# Set-up PYTHON PATH
-PYTHONPATH_ntlink=$(ntlink_path)/src/btllib/install/lib/btllib/python:$(PYTHONPATH)
-
 help:
 	@echo ""
 	@echo "ntLink: Scaffolding assemblies using long reads"
@@ -164,20 +161,20 @@ version:
 .SECONDARY:
 
 %.k$(k).w$(w).tsv: %
-	$(ntLink_time) $(ntlink_path)/src/indexlr --long --pos --strand -k $(k) -w $(w) -t $(t) $< > $@
+	$(ntLink_time) indexlr --long --pos --strand -k $(k) -w $(w) -t $(t) $< > $@
 
 %.fa.gz: %.fa
 	$(ntLink_time) $(gzip) $<
 
 $(prefix).n$(n).scaffold.dot: $(target).k$(k).w$(w).tsv $(reads)
 ifeq ($(verbose), True)
 	$(ntLink_time)  sh -c '$(gzip) -cd $(reads) | \
-	$(ntlink_path)/src/indexlr --long --pos --strand -k $(k) -w $(w) -t $(t) - | \
+	indexlr --long --pos --strand -k $(k) -w $(w) -t $(t) - | \
 	$(ntlink_path)/bin/ntlink_pair.py -p $(prefix) -n $(n) -m $< -s $(target)  \
 	-k $(k) -a $(a) -z $(z) -f $(f) -x $(x) --verbose -'
 else
 	$(ntLink_time)  sh -c '$(gzip) -cd $(reads) | \
-	$(ntlink_path)/src/indexlr --long --pos --strand -k $(k) -w $(w) -t $(t) - | \
+	indexlr --long --pos --strand -k $(k) -w $(w) -t $(t) - | \
 	$(ntlink_path)/bin/ntlink_pair.py -p $(prefix) -n $(n) -m $< -s $(target)  \
 	-k $(k) -a $(a) -z $(z) -f $(f) -x $(x) -'
 endif
@@ -199,12 +196,12 @@ endif
 	rm -f $(prefix).n*.abyss-scaffold.path $(prefix).n*.abyss-scaffold.path.sterr
 
 $(target).k$(small_k).w$(small_w).tsv: $(target)
-	$(ntLink_time) $(ntlink_path)/src/indexlr --long --pos -k $(small_k) -w $(small_w) -t $(t) $< > $@
+	$(ntLink_time) indexlr --long --pos -k $(small_k) -w $(small_w) -t $(t) $< > $@
 
 $(prefix).trimmed_scafs.fa: $(prefix).stitch.path $(prefix).n$(n).scaffold.dot $(target)
 	$(ntLink_time) sh -c '$(ntlink_path)/bin/ntlink_filter_sequences.py --fasta $(target) \
 	--dot $(prefix).n$(n).scaffold.dot --path $< -k $(small_k) -g $g |\
-	$(ntlink_path)/src/indexlr --long --pos -k $(small_k) -w $(small_w) -t $(t) - |\
+	indexlr --long --pos -k $(small_k) -w $(small_w) -t $(t) - |\
 	$(ntlink_path)/bin/ntlink_overlap_sequences.py -m -  --path $< \
 	-s $(target) -d $(prefix).n$(n).scaffold.dot -p $(prefix) -g $(g) -k $(small_k) --outgap $(merge_gap) --trim_info'
 
@@ -220,6 +217,6 @@ clean: abyss_scaffold
 	rm -f $(prefix).n*.abyss-scaffold.path $(prefix).n*.abyss-scaffold.path.sterr
 
 $(target).k$(k).w$(w).z$(z).ntLink.scaffolds.gap_fill.fa: $(target) $(prefix).n$(n).scaffold.dot $(prefix).trimmed_scafs.fa
-	PYTHONPATH=$(PYTHONPATH_ntlink) $(ntLink_time) $(ntlink_path)/bin/ntlink_patch_gaps.py --path $(prefix).trimmed_scafs.path \
+	$(ntLink_time) $(ntlink_path)/bin/ntlink_patch_gaps.py --path $(prefix).trimmed_scafs.path \
 	 --mappings $(prefix).verbose_mapping.tsv -s $< --reads $(reads) -o $@ --large_k $(k) --min_gap 1 \
 	 --trims $(prefix).trimmed_scafs.tsv -k $(gap_k) -w $(gap_w)

requirements.txt

@@ -1,2 +1,3 @@
 numpy
-python-igraph
+python-igraph
+btllib