Merge pull request #280 from rmcolq/0.9.1_branch

0.9.1

.gitignore

@@ -99,3 +99,6 @@ pandora
 #portable binary build dir
 build_portable_executable
 pandora-linux-precompiled
+
+/archives/
+/example/out/

CHANGELOG.md

@@ -9,6 +9,16 @@ project adheres to
 
 ## [Unreleased]
 
+## [0.9.1]
+
+### Added
+- `pandora` is now installable through `conda`;
+- A script to archive the `pandora` repository with git submodules;
+
+### Changed
+- Improved the sample example so now we can assert that the output produced is the expected one;
+- Changes to the build process that enables `pandora` to be compiled in the `conda` environment;
+
 ## [0.9.0]
 
 ### Changed
@@ -97,7 +107,8 @@ from this point will have their changes meticulously documented here.
 
 - k-mer coverage underflow bug in `LocalPRG` [[#183][183]]
 
-[Unreleased]: https://github.com/rmcolq/pandora/compare/0.9.0...HEAD
+[Unreleased]: https://github.com/rmcolq/pandora/compare/0.9.1...HEAD
+[0.9.1]: https://github.com/rmcolq/pandora/releases/tag/0.9.1
 [0.9.0]: https://github.com/rmcolq/pandora/releases/tag/0.9.0
 [0.9.0-rc2]: https://github.com/rmcolq/pandora/releases/tag/0.9.0-rc2
 [0.9.0-rc1]: https://github.com/rmcolq/pandora/releases/tag/0.9.0-rc1

CMakeLists.txt

@@ -1,6 +1,7 @@
 cmake_minimum_required(VERSION 3.12)  # required by hunter ZLIB installation
 
 # include hunter
+option(HUNTER_STATUS_DEBUG "Hunter debug" OFF)  # comment if does not want hunter debug on
 set(HUNTER_ROOT ${CMAKE_BINARY_DIR}/hunter)
 include("cmake/HunterGate.cmake")
 HunterGate(
@@ -11,7 +12,7 @@ HunterGate(
 
 # project configuration
 set(PROJECT_NAME_STR pandora)
-project(${PROJECT_NAME_STR} VERSION "0.9.0" LANGUAGES C CXX)
+project(${PROJECT_NAME_STR} VERSION "0.9.1" LANGUAGES C CXX)
 set(ADDITIONAL_VERSION_LABELS "")
 configure_file( include/version.h.in ${CMAKE_BINARY_DIR}/include/version.h )
 
@@ -55,8 +56,13 @@ else ()
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
 endif()
 
-# static C and C++ flags
-set(STATIC_C_CXX "-static-libgcc -static-libstdc++")
+# always link rt
+set(RT_LIBRARY "rt")
+
+if(NOT BIOCONDA)
+    # static C and C++ flags
+    set(STATIC_C_CXX "-static-libgcc -static-libstdc++")
+endif()
 
 ########################################################################################################################
 # EXTERNAL LIBS INSTALLATION
@@ -92,10 +98,10 @@ set(Gtest_LIBRARIES GTest::gtest GTest::gmock_main)
 
 ########################################################################################################################
 # INSTALL BOOST
+set(Boost_USE_STATIC_LIBS ON)
 hunter_add_package(Boost COMPONENTS filesystem iostreams log serialization system thread)
 find_package(Boost CONFIG REQUIRED filesystem iostreams log serialization system thread)
-set(BOOST_LIBRARIES Boost::filesystem Boost::iostreams Boost::log Boost::serialization Boost::system Boost::thread)
-set(Boost_USE_STATIC_LIBS ON)
+set(Boost_LIBRARIES Boost::filesystem Boost::iostreams Boost::log Boost::serialization Boost::system Boost::thread)
 ########################################################################################################################
 ########################################################################################################################
 # END EXTERNAL LIBS INSTALLATION
@@ -148,13 +154,16 @@ add_dependencies(${PROJECT_NAME} gatb)
 
 target_link_libraries(${PROJECT_NAME}
         ${GATB_LIBS}
-        ${BOOST_LIBRARIES}
+        ${Boost_LIBRARIES}
         ${ZLIB_LIBRARY}
         ${CMAKE_DL_LIBS}
         ${STATIC_C_CXX}
         ${BACKWARD_LIBRARIES}
         ${SEQAN_LIBRARIES}
+        ${RT_LIBRARY}
 )
 
 enable_testing()
 add_subdirectory(test)
+
+install(TARGETS ${PROJECT_NAME} RUNTIME DESTINATION bin)

README.md

@@ -17,6 +17,7 @@
 - [Hands-on toy example](#hands-on-toy-example)
 - [Installation](#installation)
   - [Precompiled portable binary](#no-installation-needed---precompiled-portable-binary)
+  - [Conda](#conda)
   - [Containers](#containers)
   - [Installation from source](#installation-from-source)
 - [Usage](#usage)
@@ -78,18 +79,25 @@ In this binary, all libraries are linked statically.
 
 * **Download**:
   ```
-  wget https://github.com/rmcolq/pandora/releases/download/0.9.0/pandora-linux-precompiled-v0.9.0
+  wget https://github.com/rmcolq/pandora/releases/download/0.9.1/pandora-linux-precompiled-v0.9.1
   ```
 
 * **Running**:
 ```
-chmod +x pandora-linux-precompiled-v0.9.0
-./pandora-linux-precompiled-v0.9.0 -h
+chmod +x pandora-linux-precompiled-v0.9.1
+./pandora-linux-precompiled-v0.9.1 -h
 ```
 
 * **Notes**:
   * We provide precompiled binaries for Linux OS only;
 
+### Conda
+
+To install `pandora` through `conda`, run:
+```
+conda install -c bioconda pandora
+```
+
 ### Containers
 
 [![Docker Repository on Quay](https://quay.io/repository/rmcolq/pandora/status "Docker Repository on Quay")](https://quay.io/repository/rmcolq/pandora)

example/README.md

@@ -28,18 +28,26 @@ Here we present a walkthrough of running `pandora` on a toy example. We run:
 
 ### Quick look at the output
 
-`prgs`: contains output of `make_prg from_msa` and `pandora index`. Main files:
+The output is already present in dir `out_truth`. If all went fine, the last line of the execution of the script above should be:
+
+```
+Example run produced the expected result
+```
+
+and thus the dirs `out` and `out_truth` have the same contents.
+
+`out/prgs`: contains output of `make_prg from_msa` and `pandora index`. Main files:
   * `pangenome.prg.fa`: the PRG itself;
   * `pangenome.prg.fa.k15.w14.idx` and `kmer_prgs`: the PRG index;
   * `pangenome.update_DS`: update data structures that make the PRG updateable;
 
-`pandora_discover_out`: contains the output of `pandora discover`. Main files:
+`out/pandora_discover_out`: contains the output of `pandora discover`. Main files:
   * `denovo_paths.txt`: describes the denovo paths found in all samples;
 
-`updated_prgs`: contains the output of `make_prg update` and `pandora index` (on the updated PRG).
+`out/updated_prgs`: contains the output of `make_prg update` and `pandora index` (on the updated PRG).
 The files are similar to the ones in the `prgs` folder;
 
-`output_toy_example_no_denovo` and `output_toy_example_with_denovo`: contains the output of
+`out/output_toy_example_no_denovo` and `out/output_toy_example_with_denovo`: contains the output of
 `pandora compare` without denovo discovery and with denovo discovery, respectively. Main files:
   * `pandora_multisample.matrix`: see https://github.com/rmcolq/pandora/wiki/FAQ#q-where-can-i-find-gene-presenceabsence-information ;
   * `pandora_multisample.vcf_ref.fa`: see https://github.com/rmcolq/pandora/wiki/FAQ#q-what-are-the-sequences-in-pandora_multisamplevcf_reffa
@@ -50,7 +58,7 @@ The files are similar to the ones in the `prgs` folder;
 
 **No denovo**
 
-Taking a quick look at an excerpt of `output_toy_example_no_denovo/pandora_multisample_genotyped.vcf` 
+Taking a quick look at an excerpt of `out/output_toy_example_no_denovo/pandora_multisample_genotyped.vcf`
 (the VCF genotyped by `pandora` without denovo sequences):
 
 ```
@@ -64,7 +72,7 @@ We can see samples `toy_sample_1` and `toy_sample_2` genotype towards different
 
 **With denovo**
 
-The VCF (`output_toy_example_with_denovo/pandora_multisample_genotyped.vcf`) has some new variants that were discovered and genotyped. For example:
+The VCF (`out/output_toy_example_with_denovo/pandora_multisample_genotyped.vcf`) has some new variants that were discovered and genotyped. For example:
 
 ```
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	toy_sample_1.100x.random.illumina	toy_sample_2.100x.random.illumina
@@ -73,6 +81,19 @@ GC00010897	44	.	C	T	.	.	SVTYPE=SNP;GRAPHTYPE=SIMPLE	GT:MEAN_FWD_COVG:MEAN_REV_CO
 GC00010897	422	.	A	T	.	.	SVTYPE=SNP;GRAPHTYPE=SIMPLE	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	1:0,8:0,5:0,8:0,5:0,16:0,11:1,0:-155.867,-20.2266:135.641	0:12,0:9,0:12,0:9,0:12,0:9,0:0,1:-9.39494,-182.709:173.314
 ```
 
+## Extra
+
+### Running with conda
+
+If you install `pandora` via `conda`: `conda install -c bioconda pandora`,
+you can run this sample example by activating the `conda` environment containing `pandora` and running:
+
+```
+./run_pandora.sh conda
+```
+
+The output should be the same as using the precompiled binary.
+
 <!--Link References-->
 
 [pandora_2020_paper]: https://www.biorxiv.org/content/10.1101/2020.11.12.380378v2