<div dir="ltr">Hi Barry,<div><br></div><div>Thank you for you help. I got maker running, however when I try to install it with MPI support I face some issues. I installed MPICH2 and performed the test that comes with the package and it went smoothly, however when I try to install maker the following messages appear.</div>
<div><br></div><div><br></div><div>Thank you in advance,</div><div><br></div><div>Carlos</div><div><br></div><div><div>~/maker/src$ perl Build.PL</div><div><br></div><div>MAKER supports distributed parallelization via MPI.</div>
<div>Would you like to configure MAKER for MPI (This</div><div>requires that you have an MPI client installed)? [N ]y</div><div><br></div><div>Please specify the path to 'mpicc' on your system: [/usr/bin/mpicc ]</div>
<div>/usr/bin/mpicc </div><div><br></div><div>Please specify the path to the directory containing 'mpi.h': [/usr/include/mpi ]</div><div>/usr/include/mpi </div><div><br></div><div>Would you like to install the web interface to MAKER (MWAS) on this machine</div>
<div>This requires that you be logged in as root or use sudo for './Build install'? [N ]</div><div>N </div><div>Created MYMETA.yml and MYMETA.json</div><div>Creating new 'Build' script for 'MAKER' version '2.3'</div>
<div><br></div><div><br></div><div>The file 'Build' has been created for you to finish installing MAKER.</div><div><br></div><div><br></div><div>==============================================================================</div>
<div>STATUS MAKER 2.3</div><div>==============================================================================</div><div>PERL Dependencies:<span class="" style="white-space:pre"> </span>VERIFIED</div><div>External Programs:<span class="" style="white-space:pre"> </span>VERIFIED</div>
<div>External C Libraries:<span class="" style="white-space:pre"> </span>VERIFIED</div><div>MPI SUPPORT:<span class="" style="white-space:pre"> </span>ENABLED</div><div>MWAS Web Interface:<span class="" style="white-space:pre"> </span>DISABLED</div>
<div>MAKER PACKAGE:<span class="" style="white-space:pre"> </span>CONFIGURATION OK</div><div><br></div><div><br></div><div>Important Commands:</div><div><span class="" style="white-space:pre"> </span>./Build installdeps<span class="" style="white-space:pre"> </span>#installs missing PERL dependencies</div>
<div><span class="" style="white-space:pre"> </span>./Build installexes<span class="" style="white-space:pre"> </span>#installs all missing external programs</div><div><span class="" style="white-space:pre"> </span>./Build install<span class="" style="white-space:pre"> </span>#installs MAKER</div>
<div><span class="" style="white-space:pre"> </span>./Build status<span class="" style="white-space:pre"> </span>#Shows this status menu</div><div><br></div><div>Other Commands:</div><div><span class="" style="white-space:pre"> </span>./Build repeatmasker<span class="" style="white-space:pre"> </span>#installs RepeatMasker (asks for RepBase)</div>
<div><span class="" style="white-space:pre"> </span>./Build blast<span class="" style="white-space:pre"> </span>#installs BLAST (NCBI BLAST+)</div><div><span class="" style="white-space:pre"> </span>./Build exonerate<span class="" style="white-space:pre"> </span>#installs Exonerate (v2 on UNIX / v1 on Mac OSX)</div>
<div><span class="" style="white-space:pre"> </span>./Build snap<span class="" style="white-space:pre"> </span>#installs SNAP</div><div><span class="" style="white-space:pre"> </span>./Build augustus<span class="" style="white-space:pre"> </span>#installs Augustus</div>
<div><span class="" style="white-space:pre"> </span>./Build apollo<span class="" style="white-space:pre"> </span>#installs Apollo</div><div><span class="" style="white-space:pre"> </span>./Build gbrowse<span class="" style="white-space:pre"> </span>#installs GBrowse (must be root)</div>
<div><span class="" style="white-space:pre"> </span>./Build jbrowse<span class="" style="white-space:pre"> </span>#installs JBrowse (MAKER copy, not web accecible)</div><div><span class="" style="white-space:pre"> </span>./Build webapollo<span class="" style="white-space:pre"> </span>#installs WebApollo (use maker2wap to create DBs)</div>
<div><span class="" style="white-space:pre"> </span>./Build mpich2<span class="" style="white-space:pre"> </span>#installs MPICH2 (but manual install recommended)</div><div>~/maker/src$ ./Build install</div><div>Configuring MAKER with MPI support</div>
<div>Installing MAKER...</div><div>Configuring MAKER with MPI support</div><div>Subroutine dl_load_flags redefined at (eval 93) line 8.</div><div>Installing /home/cvargas/maker/src/../perl/lib/MAKER/ConfigData.pm</div><div>
Skip /home/cvargas/maker/src/../perl/config-x86_64-linux-gnu-thread-multi-5.014002 (unchanged)</div></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Jan 13, 2014 at 10:21 PM, Barry Moore <span dir="ltr"><<a href="mailto:barry.utah@gmail.com" target="_blank">barry.utah@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Carlos,<div><br></div><div>Did you run ./Build install? If not do that first and then you want to run the copy of maker in ~/software/maker/bin/maker.</div>
<div><br></div><div>B</div><div><br></div><div><div><div><div class="h5"><div>On Jan 13, 2014, at 1:00 PM, carlos vargas wrote:</div><br></div></div><blockquote type="cite"><div><div class="h5"><div dir="ltr">Hello,<div><br>
</div><div>I have been trying to install maker but I've been facing several issues. After installing all of the prerequisites I ran perl Build.PL and ./Build install. No issues were detected. Afterwards I tried to test maker by simply executing maker -h and got the following error:</div>
<div><div><br></div><div>Can't locate MAKER/ConfigData.pm in @INC (@INC contains: ~/software/maker/src/bin/../perl/lib ~/software/maker/src/bin/../lib ~/software/maker/src/bin/../src/inc/perl/lib /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at ~/software/maker/src/bin/maker line 42.</div>
<div>BEGIN failed--compilation aborted at ~/software/maker/src/bin/maker line 42.</div><div><br></div><div>I found a similar thread which suggested reinstalling (which I did) but I still face the same issue. The full messages are below.</div>
<div><br></div><div><br></div><div>Thank you for your help!</div><div><br></div><div>Carlos</div><div><br></div><div><br></div><div><div>~/software/maker/src$ sudo perl Build.PL</div><div><br></div><div>MAKER supports distributed parallelization via MPI.</div>
<div>Would you like to configure MAKER for MPI (This</div><div>requires that you have an MPI client installed)? [N ]</div><div>N</div><div><br></div><div>Would you like to install the web interface to MAKER (MWAS) on this machine</div>
<div>This requires that you be logged in as root or use sudo for './Build install'? [N ]</div><div>N</div><div>Created MYMETA.yml and MYMETA.json</div><div>Creating new 'Build' script for 'MAKER' version '2.3'</div>
<div><br></div><div><br></div><div>The file 'Build' has been created for you to finish installing MAKER.</div><div><br></div><div><br></div><div>==============================================================================</div>
<div>STATUS MAKER 2.3</div><div>==============================================================================</div><div>PERL Dependencies: VERIFIED</div><div>External Programs: VERIFIED</div><div>External C Libraries: VERIFIED</div>
<div>MPI SUPPORT: DISABLED</div><div>MWAS Web Interface: DISABLED</div><div>MAKER PACKAGE: CONFIGURATION OK</div><div><br></div><div><br></div><div>Important Commands:</div><div> ./Build installdeps #installs missing PERL dependencies</div>
<div> ./Build installexes #installs all missing external programs</div><div> ./Build install #installs MAKER</div><div> ./Build status #Shows this status menu</div><div><br></div>
<div>Other Commands:</div><div> ./Build repeatmasker #installs RepeatMasker (asks for RepBase)</div><div> ./Build blast #installs BLAST (NCBI BLAST+)</div><div> ./Build exonerate #installs Exonerate (v2 on UNIX / v1 on Mac OSX)</div>
<div> ./Build snap #installs SNAP</div><div> ./Build augustus #installs Augustus</div><div> ./Build apollo #installs Apollo</div><div> ./Build gbrowse #installs GBrowse (must be root)</div>
<div> ./Build jbrowse #installs JBrowse (MAKER copy, not web accecible)</div><div> ./Build webapollo #installs WebApollo (use maker2wap to create DBs)</div><div> ./Build mpich2 #installs MPICH2 (but manual install recommended)</div>
<div><br></div><div>~/software/maker/src$ sudo ./Build install</div><div>Building MAKER</div><div>Installing MAKER...</div><div>Building MAKER</div><div>Installing ~/software/maker/src/../perl/lib/MAKER/ConfigData.pm</div>
<div><br></div><div>~/software/maker/src$ maker -h</div><div>Can't locate MAKER/ConfigData.pm in @INC (@INC contains: ~/software/maker/src/bin/../perl/lib ~/software/maker/src/bin/../lib ~/software/maker/src/bin/../src/inc/perl/lib /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at ~/software/maker/src/bin/maker line 42.</div>
<div>BEGIN failed--compilation aborted at ~/software/maker/src/bin/maker line 42.</div><div><br></div></div><div><br></div></div></div></div></div><div class="im">
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</div></blockquote></div><span class="HOEnZb"><font color="#888888"><br><div>
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<span style="font-family:Arial;font-size:12px"><div>Barry Moore</div><div>Research Scientist</div><div>Dept. of Human Genetics</div><div>University of Utah</div><div>Salt Lake City, UT 84112</div><div>--------------------------------------------</div>
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