Commit 7868af61 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.11.1

parent 64e79bf2

.gitignore

+1 −1
Original line number Diff line number Diff line
@@ -17,7 +17,7 @@ include/ 
lib/

share/



hdf5-1.8.14.tar.gz

hdf5-1.*.tar.gz

3.2.5.tar.bz2

eigen/

local*

.travis.yml

+72 −14
Original line number Diff line number Diff line 
# travis.yml for github.com/jts/nanopolish



dist: trusty

services: docker

sudo: false

language: generic

cache: apt

git:

    depth: 1



.nanopolish.ci.matrix-definitions:

    - &cron-only

      if: type = cron OR env(CI_CRON) = true

    - &arch

      before_install:

          - |

            sed -i "/^FROM / s/arm64/${ARCH}/" Dockerfile-arm

          - |

            docker run --rm --privileged \

                multiarch/qemu-user-static:register --reset && \

                docker build --rm -t nanopolish -f Dockerfile-arm .

      script:

          - |

            docker run --rm -t \

                -e HDF5="${HDF5:-install}" \

                -e H5_CFLAGS="${H5_CFLAGS}" \

                -e H5_INCLUDE="${H5_INCLUDE}" \

                -e LDFLAGS="${LDFLAGS}" \

                nanopolish



matrix:

    include:

        # Set env for both nanoplish and the dependency hdf5.
@@ -22,6 +43,41 @@ matrix: 
              - AR=gcc-ar-8

              - NM=gcc-nm-8

              - RANLIB=gcc-ranlib-8

        # aarch64 - ARM 64-bit

        - name: aarch64

          sudo: required

          env:

              - ARCH=arm64

          <<: *arch

          <<: *cron-only

        - name: aarch64-system-hdf5

          sudo: required

          env:

              - ARCH=arm64

              - HDF5="system"

              - H5_INCLUDE="-I/usr/include/hdf5/serial"

              - LDFLAGS="-L/usr/lib/aarch64-linux-gnu/hdf5/serial"

          <<: *arch

        # armv7l - ARM 32-bit

        - name: armv7l

          sudo: required

          env:

              - ARCH=armhf

          <<: *arch

          <<: *cron-only

        - name: armv7l-system-hdf5

          sudo: required

          env:

              - ARCH=armhf

              - HDF5="system"

              - H5_INCLUDE="-I/usr/include/hdf5/serial"

              - LDFLAGS="-L/usr/lib/arm-linux-gnueabihf/hdf5/serial"

          <<: *arch

    allow_failures:

        # The jobs installing hdf5 from source in docker finishes with error

        # because of the job exceeded the maximum time limit (50 minutes).

        - name: aarch64

        - name: armv7l



# Install and export newer gcc

before_install:
@@ -38,9 +94,11 @@ before_install: 
          sudo apt-get install -qq "${CXX}"

      fi



script:

before_script:

    # Suppress all compiler warnings for hdf5 Makefile

    # to display the log without downloading the raw log on Travis log page.

    # Travis finishs with error when exceeding the limit of 4 MB of log length.

    - export H5_CFLAGS="-w"



script:

    - make && make test

Dockerfile-arm

0 → 100644
+18 −0
Original line number Diff line number Diff line 
FROM multiarch/ubuntu-debootstrap:arm64-bionic

RUN uname -a

RUN apt-get update -qq && \

  apt-get install -yq --no-install-suggests --no-install-recommends \

  bzip2 \

  ca-certificates \

  gcc \

  g++ \

  make \

  software-properties-common

RUN add-apt-repository -y universe && \

  apt-get update -qq && \

  apt-get install -yq libhdf5-dev

RUN find /usr/include -name "hdf5.h" || true

RUN find /usr/lib -name "libhdf5.a" || true

WORKDIR /nanopolish

COPY . .

CMD exec bash -c "make && make test"

Makefile

+6 −6
Original line number Diff line number Diff line
@@ -12,6 +12,7 @@ LIBS = -lz 
CXXFLAGS ?= -g -O3

CXXFLAGS += -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 #D_FILE_OFFSET_BITS=64 makes nanopolish work in 32 bit systems

CFLAGS ?= -O3 -std=c99 -fsigned-char -D_FILE_OFFSET_BITS=64 

LDFLAGS ?=

CXX ?= g++

CC ?= gcc
@@ -20,8 +21,7 @@ HDF5 ?= install 
EIGEN ?= install

HTS ?= install



HDF5_VERSION ?= 1.8.14

HDF5_CONFIG_ARGS ?= --enable-threadsafe

HDF5_VERSION ?= 1.10.4

EIGEN_VERSION ?= 3.2.5



# Check operating system, OSX doesn't have -lrt
@@ -38,7 +38,7 @@ ifeq ($(HDF5), install) 
else

    # Use system-wide hdf5

    H5_LIB =

    H5_INCLUDE =

    H5_INCLUDE ?=

    LIBS += -lhdf5

endif
@@ -91,13 +91,13 @@ htslib/libhts.a: 
#

lib/libhdf5.a:

	if [ ! -e hdf5-$(HDF5_VERSION).tar.gz ]; then \

		version_major_minior=`echo "$(HDF5_VERSION)" | sed -E 's/\.[0-9]+$$//'`; \

		wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$${version_major_minior}/hdf5-$(HDF5_VERSION)/src/hdf5-$(HDF5_VERSION).tar.gz; \

		version_major_minor=`echo "$(HDF5_VERSION)" | sed -E 's/\.[0-9]+$$//'`; \

		wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$${version_major_minor}/hdf5-$(HDF5_VERSION)/src/hdf5-$(HDF5_VERSION).tar.gz; \

	fi



	tar -xzf hdf5-$(HDF5_VERSION).tar.gz || exit 255

	cd hdf5-$(HDF5_VERSION) && \

        ./configure --enable-threadsafe --libdir=`pwd`/../lib --includedir=`pwd`/../include --prefix=`pwd`/.. && \

		./configure --enable-threadsafe --disable-hl --libdir=`pwd`/../lib --includedir=`pwd`/../include --prefix=`pwd`/.. && \

		make && make install



# Download and install eigen if not already downloaded

docs/source/index.rst

+1 −0
Original line number Diff line number Diff line
@@ -15,6 +15,7 @@ nanopolish 
   quickstart_consensus

   quickstart_eventalign

   quickstart_call_methylation

   quickstart_polya

   debug

   manual