Hap.py installation error

[pinninti19]

Hi, not able to install hap.py

git clone https://github.com/sequencing/hap.py
mkdir hap.py-build
cd hap.py-build
Run CMake
cmake ../hap.py
Build
make

After make it showing error, can any one help me with installation ?

jsoncpp.cpp:(.text.ZN4Json6Reader15StructuredErrorC2EOS1[ZN4Json6Reader15StructuredErrorC5EOS1]+0x45): undefined reference to `std::__cxx11::basic_string<char, std::char_traits, std::allocator >::basic_string(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&&)' collect2: error: ld returned 1 exit status make[2]: [src/c++/main/CMakeFiles/xcmp.dir/build.make:111: bin/xcmp] Error 1 make[1]: [CMakeFiles/Makefile2:304: src/c++/main/CMakeFiles/xcmp.dir/all] Error 2 make: *** [Makefile:128: all] Error 2

[pkrusche]

Hi, could you perhaps post some details on your system + compiler versions?

Do you have an installation of libstdc++-dev? It seems that it is trying to link only with a C compiler, or that there is no C++ STL library installed.

[pinninti19]

Firstly, thanks for reply. I had GCC already installed. Find the attached.

Best,

On Mon, Feb 5, 2018 at 4:23 PM, Peter Krusche notifications@github.com wrote:

Hi, could you perhaps post some details on your system + compiler versions?

Do you have an installation of libstdc++-dev? It seems that it is trying to link only with a C compiler, or that there is no C++ STL library installed.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Illumina/hap.py/issues/39#issuecomment-363049645, or mute the thread https://github.com/notifications/unsubscribe-auth/AhZ_lwl0a_wRKSxTp0Xa87xw1WLS3hLbks5tRt2XgaJpZM4R4HFZ .

[pkrusche]

Hi, I think your email attachment didn't get picked up by github -- could you please try to upload it on the Github issue directly?

Depending on your system / distribution, you will need to have installations of gcc, g++ and libc++ or libstdc++ (-devel packages s.t. headers are available). GCC needs to be newer than 4.9.x.

[pinninti19]

Hi

again error (I installed gcc, g++ and libc ++) jsoncpp.cpp:(.text.ZN4Json6Reader15StructuredErrorC2EOS1[ZN4Json6Reader15StructuredErrorC5EOS1]+0x45): undefined reference to `std::__cxx11::basic_string<char, std::char_traits, std::allocator

::basic_string(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&&)' collect2: error: ld returned 1 exit status make[2]: [src/c++/main/CMakeFiles/xcmp.dir/build.make:111: bin/xcmp] Error 1 make[1]: [CMakeFiles/Makefile2:304: src/c++/main/CMakeFiles/xcmp.dir/all] Error 2 make: *** [Makefile:128: all] Error 2

On Tue, Feb 6, 2018 at 3:59 PM, Peter Krusche notifications@github.com wrote:

Hi, I think your email attachment didn't get picked up by github -- could you please try to upload it on the Github issue directly?

Depending on your system / distribution, you will need to have installations of gcc, g++ and libc++ or libstdc++ (-devel packages s.t. headers are available). GCC needs to be newer than 4.9.x.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Illumina/hap.py/issues/39#issuecomment-363379672, or mute the thread https://github.com/notifications/unsubscribe-auth/AhZ_l9HnYQ5h5-aE2KVdsHwOfg9CSu6lks5tSCl_gaJpZM4R4HFZ .

[pkrusche]

Which system (Linux distribution / MacOS version?) are you working on? A full list of dependencies for Ubuntu can be found in the Dockerfile here: https://github.com/Illumina/hap.py/blob/master/Dockerfile

[pinninti19]

I'm working on ubuntu 16.04LTS

On Tue, Feb 6, 2018 at 7:55 PM, Peter Krusche notifications@github.com wrote:

Which system (Linux distribution / MacOS version?) are you working on? A full list of dependencies for Ubuntu can be found in the Dockerfile here: https://github.com/Illumina/hap.py/blob/master/Dockerfile

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Illumina/hap.py/issues/39#issuecomment-363437518, or mute the thread https://github.com/notifications/unsubscribe-auth/AhZ_l8JEksgpHTF72deCRYgevmEwp89Mks5tSGDmgaJpZM4R4HFZ .

[pkrusche]

The Dockerfile should show all the packages you need then -- I think by default Ubuntu may not come with all development tools and libraries needed for hap.py. Could you please check that you have all the following libraries installed:

build-essential 
zlib1g-dev
libbz2-dev
pkg-config
cmake
libncurses5-dev
autoconf
git
bzip2 
wget
python2.7
python2.7-dev
python
python-setuptools 
python-pip 
python-psutil 
cython 
python-numpy 
python-pandas 
python-distribute 
python-pysam 
python-scipy 
software-properties-common
python-software-properties

[pkrusche]

Another issue may be that you need to delete the build folder for Cmake and start from scratch -- Cmake can get confused when additional packages / compilers appear between builds.

[pinninti19]

Hi Peter I installed, using docker. The hap.py only only runs with a reference hg19 ?

On Tue, Feb 6, 2018 at 8:00 PM, Peter Krusche notifications@github.com wrote:

Another issue may be that you need to delete the build folder for Cmake and start from scratch -- Cmake can get confused when additional packages / compilers appear between builds.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Illumina/hap.py/issues/39#issuecomment-363438993, or mute the thread https://github.com/notifications/unsubscribe-auth/AhZ_l1Hg2Sqa8vgWKSbE8CCawVRtQN5Wks5tSGIQgaJpZM4R4HFZ .

[pkrusche]

You can specify a different reference fasta using the -r command line switch. Note that the reference fasta must be the same for all input files (truth, query, any bed file).

[pinninti19]

Its showing error, confidence and bed file downloaded from ncbi-ftp site.

bed file - HG005_GRCh38 confidence vcf - HG005_GRCh38 (Chinese son) qury vcf - exome vcf (1000 g dataset)

root@f81419609198:/opt/hap.py/bin# ./hap.py /home/likithreddy/Documents/Genome/confidencecalls/Latestconfidencecalls/ChineseSon/HG005_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC-SOLIDgatkHC_CHROM1-22_v.3.3.2_highconf.vcf /home/likithreddy/Documents/Genome/vcf/SRR098401.Aligner.freebayes.raw.SNV.vcf -f /home/likithreddy/Documents/Genome/confidencecalls/Latestconfidencecalls/ChineseSon/HG005_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC-SOLIDgatkHC_CHROM1-22_v.3.3.2_highconf.bed -o outputson -r /home/likithreddy/Documents/Genome/hg38.fa 2018-02-07 15:23:32,691 WARNING No reference file found at default locations. You can set the environment variable 'HGREF' or 'HG19' to point to a suitable Fasta file. 2018-02-07 15:23:32,692 WARNING No reference file found at default locations. You can set the environment variable 'HGREF' or 'HG19' to point to a suitable Fasta file. 2018-02-07 15:23:32,796 ERROR FP/confident call region bed file does not exist. 2018-02-07 15:23:32,797 ERROR Traceback (most recent call last): 2018-02-07 15:23:32,797 ERROR File "./hap.py", line 508, in 2018-02-07 15:23:32,797 ERROR main() 2018-02-07 15:23:32,797 ERROR File "./hap.py", line 198, in main 2018-02-07 15:23:32,797 ERROR raise Exception("FP/confident call region bed file does not exist.") 2018-02-07 15:23:32,797 ERROR Exception: FP/confident call region bed file does not exist.

Thanks

On Wed, Feb 7, 2018 at 8:48 PM, Peter Krusche notifications@github.com wrote:

You can specify a different reference fasta using the -r command line switch. Note that the reference fasta must be the same for all input files (truth, query, any bed file).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Illumina/hap.py/issues/39#issuecomment-363801534, or mute the thread https://github.com/notifications/unsubscribe-auth/AhZ_lzX-xbgZxvMbCvRGjHZQCoRDQbhnks5tSb7cgaJpZM4R4HFZ .

[pkrusche]

The reference file is not the problem (the reference-related messages are just warnings), it seems the confident region file path does not exist. Have you mounted your home folder inside Docker using -v, and does the file exist?

[pinninti19]

I don't have any idea, how to mount docker ?

On Wed, Feb 7, 2018 at 9:01 PM, Peter Krusche notifications@github.com wrote:

The reference file is not the problem (the reference-related messages are just warnings), it seems the confident region file path does not exist. Have you mounted your home folder inside Docker using -v, and does the file exist?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Illumina/hap.py/issues/39#issuecomment-363805636, or mute the thread https://github.com/notifications/unsubscribe-auth/AhZ_l0CgQ3K0S9y5Sm3QLIy8g5N8Zgbxks5tScHMgaJpZM4R4HFZ .

[pkrusche]

When you run docker, run it with -v /home/likithreddy:/home/likithreddy -- this will make your home directory available inside Docker. See here: https://stackoverflow.com/questions/23439126/how-to-mount-host-directory-in-docker-container

[pinninti19]

Thanks! hap.py working.

On Thu, Feb 8, 2018 at 2:27 PM, Peter Krusche notifications@github.com wrote:

When you run docker, run it with -v /home/likithreddy:/home/likithreddy -- this will make your home directory available inside Docker. See here: https://stackoverflow.com/questions/23439126/how-to- mount-host-directory-in-docker-container

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Illumina/hap.py/issues/39#issuecomment-364044670, or mute the thread https://github.com/notifications/unsubscribe-auth/AhZ_lzE3SdMBTq7DOGLrefceZqAQCvRYks5tSrcEgaJpZM4R4HFZ .

[pkrusche]

Great, happy to hear!

[pinninti19]

Hi

I run the hap.py for my vcf. I can understand the output table. I wish to do roc plot (Precision vs sensitivity) so, which file should i give as input ? I had 4 vcf from one dataset with different variant calling process. Thanks!

On Fri, Feb 9, 2018 at 4:48 PM, Peter Krusche notifications@github.com wrote:

Great, happy to hear!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Illumina/hap.py/issues/39#issuecomment-364407255, or mute the thread https://github.com/notifications/unsubscribe-auth/AhZ_l-WLZkgUBaG_4_8dZoLfZRY_tChIks5tTCmLgaJpZM4R4HFZ .

[pinninti19]

Could you please tell me the difference between the hap.py and RTG tool. Both of them do the same job isn't ?

On Sat, Feb 10, 2018 at 6:06 PM, LIKITH Reddy pinninti1991reddy@gmail.com wrote:

Hi

I run the hap.py for my vcf. I can understand the output table. I wish to do roc plot (Precision vs sensitivity) so, which file should i give as input ? I had 4 vcf from one dataset with different variant calling process. Thanks!

On Fri, Feb 9, 2018 at 4:48 PM, Peter Krusche notifications@github.com wrote:

Great, happy to hear!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Illumina/hap.py/issues/39#issuecomment-364407255, or mute the thread https://github.com/notifications/unsubscribe-auth/AhZ_l-WLZkgUBaG_4_8dZoLfZRY_tChIks5tTCmLgaJpZM4R4HFZ .

[pkrusche]

To create plots + analysis, we have published a separate R package here: https://github.com/illumina/happyR -- this has some documentation also. Also, the GA4GH benchmarking toolset contains scripts for interactive reporting based on hap.py results: https://github.com/ga4gh/benchmarking-tools/tree/master/reporting/basic

RTG vcfeval can be used inside hap.py to compare variants. It will become the default option in the next version. The main added value of hap.py is that it provides preprocessing, stratification and a more detailed breakdown of metrics. Also, hap.py facilitates running comparisons that follow the GA4GH best-practices for variant benchmarking.