{"id":1051,"date":"2011-09-07T11:02:09","date_gmt":"2011-09-07T09:02:09","guid":{"rendered":"http:\/\/oldblogs.uct.ac.za\/blog\/big-bytes\/2011\/09\/07\/compiling-abyss"},"modified":"2015-08-14T13:22:35","modified_gmt":"2015-08-14T11:22:35","slug":"compiling-abyss","status":"publish","type":"post","link":"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/09\/07\/compiling-abyss\/","title":{"rendered":"Compiling ABySS"},"content":{"rendered":"From the ABySS web site<\/a><\/em>: ABySS (Assembly By Short Sequences) is a de novo<\/em>,\r\nparallel, paired-end sequence assembler that is designed for short\r\nreads. The single-processor version is useful for assembling genomes up\r\nto 100 Mbases in size. The parallel version is implemented using MPI and\r\nis capable of assembling larger genomes.\r\n\r\nWe decided to document the installation of ABySS 1.2.7\r\n\r\nFirst, you will need to download a dependency called \" Sparsehash \". The download can be found here. <\/a>\r\n\r\nGoogle Sparsehash Installation <\/span><\/strong>\r\nIf you have administrative permissions then follow this section\r\n- .\/configure\r\n- make\r\n- make install\r\n\r\nNB: This install the sparse hash into \/usr\/local\/include\r\n\r\nFor non administrative users\r\n- .\/configure --prefix=$HOME\/user\r\n- make\r\n- make install\r\n\r\nABySS Installation\u00a0<\/span><\/strong>\r\n\r\nDownload <\/a>\r\n\r\n- .\/configure --prefix=\/opt\/exp_soft\/sagrid\/abyss-1.2.7 --with-mpi=\/usr\/lib64\/openmpi CPPFLAGS=-I\/opt\/exp_soft\/sagrid\/abyss-1.2.7\/google-sparsehash-1.11\/include<\/strong>\r\n\r\nThe CPPFLAGS entry is used to reference the location of the dependency installed earlier.\r\n\r\nNB: Ensure that the following is correct before continuation. The config.log file generated during the compile will indicate if the CPPFLAGS entry was successfully used.\r\n\r\nchecking google\/sparse_hash_map usability... yes\r\nchecking google\/sparse_hash_map presence... yes\r\nchecking for google\/sparse_hash_map... yes<\/em><\/strong>\r\n\r\n- make <\/strong>\r\n\r\nIf you are running a earlier version of GCC you would see an error to the effect of \" \"cc1plus: warnings being treated as errors\r\nDistanceEst.cpp:392: warning: ignoring #pragma omp task \"\r\nUpdate your make command with :\r\n\r\n- make AM_CXXFLAGS=-Wall\r\n- make install <\/strong>\r\n\r\nInstallation is now complete and access path to the binary is available at - \/opt\/exp_soft\/sagrid\/abyss-1.2.7 - or whichever location you have made available in your --prefix=.","protected":false},"excerpt":{"rendered":"

From the ABySS<\/span> web site<\/a><\/em>: ABySS<\/span> (Assembly By Short Sequences) is a de novo<\/em>,
\n parallel, paired-end sequence assembler that is designed for short
\nreads. The single-processor version is useful for assembling genomes up
\nto 100 Mbases in size. The parallel version is implemented using MPI and
\n is capable of assembling larger genomes.\n<\/p>\n

We decided to document the installation of ABySS 1.2.7 <\/p>\n

First, you will need to download a dependency called ” Sparsehash “. The download can be found here. <\/a><\/p>\n

Google Sparsehash Installation <\/span><\/strong>
If you have administrative permissions then follow this section
        – .\/configure
        – make
        – make install <\/p>\n

NB: This install the sparse hash into \/usr\/local\/include
   
For non administrative users
        – .\/configure –prefix=$HOME\/user
        – make
        – make install  <\/p>\n

ABySS Installation <\/span><\/strong><\/p>\n

Download <\/a><\/p>\n

 – .\/configure –prefix=\/opt\/exp_soft\/sagrid\/abyss-1.2.7 –with-mpi=\/usr\/lib64\/openmpi CPPFLAGS=-I\/opt\/exp_soft\/sagrid\/abyss-1.2.7\/google-sparsehash-1.11\/include<\/strong><\/p>\n

The CPPFLAGS entry is used to reference the location of the dependency installed earlier.<\/p>\n

NB: Ensure that the following is correct before continuation. The config.log file generated during the compile will indicate if the CPPFLAGS entry was successfully used.  <\/p>\n

checking google\/sparse_hash_map usability… yes
checking google\/sparse_hash_map presence… yes
checking for google\/sparse_hash_map… yes<\/em><\/strong><\/p>\n

– make <\/strong><\/p>\n

 If you are running a earlier version of GCC you would see an error to the effect of ” “cc1plus: warnings being treated as errors
DistanceEst.cpp:392: warning: ignoring #pragma omp task “
Update your make command with :<\/p>\n

– make AM_CXXFLAGS=-Wall
– make install <\/strong><\/p>\n

Installation is now complete and access path to the binary is available at – \/opt\/exp_soft\/sagrid\/abyss-1.2.7 – or whichever location you have made available in your –prefix=.<\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[9],"tags":[],"yoast_head":"\nCompiling ABySS - UCT HPC<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/09\/07\/compiling-abyss\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Compiling ABySS - UCT HPC\" \/>\n<meta property=\"og:description\" content=\"From the ABySS web site: ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. We decided to document the installation of ABySS 1.2.7 First, you will need to download a dependency called " Sparsehash ". The download can be found here. Google Sparsehash Installation If you have administrative permissions then follow this section         - .\/configure         - make         - make install NB: This install the sparse hash into \/usr\/local\/include     For non administrative users        - .\/configure --prefix=$HOME\/user         - make         - make install  ABySS Installation Download  - .\/configure --prefix=\/opt\/exp_soft\/sagrid\/abyss-1.2.7 --with-mpi=\/usr\/lib64\/openmpi CPPFLAGS=-I\/opt\/exp_soft\/sagrid\/abyss-1.2.7\/google-sparsehash-1.11\/includeThe CPPFLAGS entry is used to reference the location of the dependency installed earlier.NB: Ensure that the following is correct before continuation. The config.log file generated during the compile will indicate if the CPPFLAGS entry was successfully used.  checking google\/sparse_hash_map usability... yeschecking google\/sparse_hash_map presence... yeschecking for google\/sparse_hash_map... yes- make  If you are running a earlier version of GCC you would see an error to the effect of " "cc1plus: warnings being treated as errorsDistanceEst.cpp:392: warning: ignoring #pragma omp task "Update your make command with :- make AM_CXXFLAGS=-Wall- make install Installation is now complete and access path to the binary is available at - \/opt\/exp_soft\/sagrid\/abyss-1.2.7 - or whichever location you have made available in your --prefix=.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/09\/07\/compiling-abyss\/\" \/>\n<meta property=\"og:site_name\" content=\"UCT HPC\" \/>\n<meta property=\"article:published_time\" content=\"2011-09-07T09:02:09+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2015-08-14T11:22:35+00:00\" \/>\n<meta name=\"author\" content=\"Timothy Carr\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Timothy Carr\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/09\/07\/compiling-abyss\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/09\/07\/compiling-abyss\/\"},\"author\":{\"name\":\"Timothy Carr\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#\/schema\/person\/41f6cd039836d7741f2b82a7b7cfe8d0\"},\"headline\":\"Compiling ABySS\",\"datePublished\":\"2011-09-07T09:02:09+00:00\",\"dateModified\":\"2015-08-14T11:22:35+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/09\/07\/compiling-abyss\/\"},\"wordCount\":282,\"publisher\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#organization\"},\"articleSection\":[\"application\"],\"inLanguage\":\"en-ZA\"},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/09\/07\/compiling-abyss\/\",\"url\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/09\/07\/compiling-abyss\/\",\"name\":\"Compiling ABySS - 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