dockerfile, ci and v1.2.7

.travis.yml

@@ -1,26 +1,26 @@
 dist: xenial
 before_install:
   - sudo apt-get update
-  - sudo apt-get install lcov
+  - sudo apt-get install -y lcov
 language: python
 python:
   - "2.7"
   - "3.4"
 script:
   - mkdir build
-  - cd build && cmake .. -DCMAKE_BUILD_TYPE=Debug -DCOVERAGE=ON
+  - cd build && cmake .. -DCOVERAGE=ON
   - make -j2 simple_test
   - sudo make install
   - megahit --test
   - megahit --test --kmin-1pass
   - megahit --test --no-hw-accel
 after_success:
   # Create lcov report
-  - lcov --capture --directory . --output-file coverage.info
-  - lcov --remove coverage.info '/usr/*' --output-file coverage.info # filter system-files
-  - lcov --remove coverage.info '*xxhash/*' --output-file coverage.info # filter xxhash-files
-  - lcov --remove coverage.info '*parallel_hashmap/*' --output-file coverage.info # filter parallel-hashmap-files
-  - lcov --remove coverage.info '*pprintpp/*' --output-file coverage.info # filter pprintpp files
-  - lcov --list coverage.info # debug info
+  - lcov --capture --directory . --output-file coverage.info.1
+  - lcov --remove coverage.info.1 '/usr/*' --output-file coverage.info.2 # filter system-files
+  - lcov --remove coverage.info.2 '*xxhash/*' --output-file coverage.info.3 # filter xxhash-files
+  - lcov --remove coverage.info.3 '*parallel_hashmap/*' --output-file coverage.info.4 # filter parallel-hashmap-files
+  - lcov --remove coverage.info.4 '*pprintpp/*' --output-file coverage.info.5 # filter pprintpp files
+  - lcov --list coverage.info.5 # debug info
   # Uploading report to CodeCov
-  - bash <(curl -s https://codecov.io/bash) -f coverage.info || echo "Codecov did not collect coverage reports"
+  - bash <(curl -s https://codecov.io/bash) -f coverage.info.5 || echo "Codecov did not collect coverage reports"

CHANGELOG.md

@@ -1,3 +1,9 @@
+### 1.2.7 / 2019-07-28
+-   Symbol link `megahit_core_no_hw_accel` to `megahit_toolkit` for backward compatibility
+-   Better logging and for memory adjustment during SDBG building
+-   Attempt to continue SDBG building even user-specified memory size is not sufficient
+
+
 ### 1.2.6 / 2019-07-13
 -   Refactored and fixed a bug in local assembler
 -   Refactored `megahit` script

Dockerfile

@@ -8,7 +8,6 @@ RUN mkdir -p build
 WORKDIR build
 RUN cmake -DCMAKE_BUILD_TYPE=Release ..
 RUN make -j4
-RUN make simple_test
 RUN make install
 RUN megahit --test
 RUN megahit --test --kmin-1pass

README.md

@@ -8,26 +8,31 @@ MEGAHIT is an ultra-fast and memory-efficient NGS assembler. It is optimized for
 Installation
 ---------------
 
-#### Prebuilt binaries for x86_64 Linux
+### Conda
+```sh
+conda install -c bioconda megahit
+```
+
+### Pre-built binaries for x86_64 Linux
 
 ```sh
-wget https://github.com/voutcn/megahit/releases/download/v1.2.6/MEGAHIT-1.2.6-Linux-x86_64-static.tar.gz
-tar zvxf MEGAHIT-1.2.6-Linux-x86_64-static.tar.gz
-cd MEGAHIT-1.2.6-Linux-x86_64-static/bin/
+wget https://github.com/voutcn/megahit/releases/download/v1.2.7/MEGAHIT-1.2.7-Linux-x86_64-static.tar.gz
+tar zvxf MEGAHIT-1.2.7-Linux-x86_64-static.tar.gz
+cd MEGAHIT-1.2.7-Linux-x86_64-static/bin/
 ./megahit --test  # run on a toy dataset
 ./megahit -1 MY_PE_READ_1.fq.gz -2 MY_PE_READ_2.fq.gz -o MY_OUTPUT_DIR
 ```
 
-#### Prebuilt Docker image
+### Pre-built docker image
 ``` sh
-# in the directory with your input reads
+# in the directory with the input reads
 docker run -v $(pwd):/workspace -w /workspace --user $(id -u):$(id -g) vout/megahit \
   megahit -1 MY_PE_READ_1.fq.gz -2 MY_PE_READ_2.fq.gz -o MY_OUTPUT_DIR
 ```
 
-#### Building from source
+### Building from source
 
-##### Prerequisites
+#### Prerequisites
 
 -   For building: zlib, cmake >= 2.8, g++ >= 4.8.4
 -   For running: gzip and bzip2
@@ -37,7 +42,7 @@ git clone https://github.com/voutcn/megahit.git
 cd megahit
 git submodule update --init
 mkdir build && cd build
-cmake .. -DCMAKE_BUILD_TYPE=Release  # add -DCMAKE_INSTALL_PREFIX=YOUR_PREFIX if needed
+cmake .. -DCMAKE_BUILD_TYPE=Release  # add -DCMAKE_INSTALL_PREFIX=MY_PREFIX if needed
 make -j4
 make simple_test  # will test MEGAHIT with a toy dataset
 # make install if needed
@@ -46,7 +51,7 @@ make simple_test  # will test MEGAHIT with a toy dataset
 Usage
 -----
 
-#### Basic usage
+### Basic usage
 ```sh
 megahit -1 pe_1.fq -2 pe_2.fq -o out  # 1 paired-end library
 megahit --12 interleaved.fq -o out # one paired & interleaved paired-end library
@@ -55,7 +60,7 @@ megahit_core contig2fastg 119 out/intermediate_contigs/k119.contig.fa > k119.fas
 ```
 The contigs can be found `final.contigs.fa` in the output directory.
 
-#### Advanced usage
+### Advanced usage
 - `--kmin-1pass`: if sequencing depth is low and too much memory used when build the graph of k_min
 - `--presets meta-large`: if the metagenome is complex (i.e., bio-diversity is high, for example soil metagenomes)
 - `--cleaning-rounds 1 --disconnect-ratio 0`: get less pruned assembly (usually shorter contigs)
@@ -74,4 +79,4 @@ Publications
 License
 -------
 
-This project is licensed under the GPLv3 License - see the [LICENSE](LICENSE) file for details
+This project is licensed under the GPLv3 License - see the [LICENSE](LICENSE) file for details