Tag Archives: troubleshooting

NEB HF enzymes – regarding library preps

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Hi guys,

Just a note about PstI-HF:

The PstI-HF sold from NEB is less processive than the old NEB PstI/red stripe version (go here to see it: https://www.neb.com/products/r0140-psti) .  When digesting ultrapure, high concentration homogeneous DNA (plasmids) digestions fail to go to completion even when left overnight (> 16 hours).  What does this mean for you?  It means that your genomes which are more difficult substrates to deal with will not digest fully unless left to go overnight.  If you want to ensure a good digest use a positive control and switch to the linked product.

 

 

 

 

C/C++ Dependency Troubleshooting

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Unix C/C++ programs are very finicky about the compiler and library versions.  Compiling is the process of translating human readable code into a binary executable or library that contains machine-friendly instructions.  Linking is the process of telling multiple executables or libraries how to talk to each other.

gcc is a GNU C compiler that is typically used on unix systems. g++ is a GNU C++ compiler on unix systems.  libstdc++ is the GNU standard C++ library.   glibc is the GNU standard C library.  When you install GCC on your unix machine, you are installing a package of the aforementioned items.  The gcc unix command is smart enough to call either the gcc compiler or g++ compiler depending if you pass it C or C++ code.

If you attempt to run your program with an older standard library than it was originally linked it with, your program will crash and complain.  Here are some tips to get around it.

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C / C++ Troubleshooting

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IN PROGRESS

Most of the high-performance bioinformatic programs are written in C or C++.  Unfortunately, C and C++ code is some of the hardest code to debug.  If you have only programmed casually in perl/python, you will not have a good time.  Here are some tips to help you out, but you will most likely need someone with C / C++ programming experience and knowledge of the code to get you through it.

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Perl Troubleshooting

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This is a collection of fixes for various issues I’ve had with Perl.  Feel free to add any of your Perl tips here.  I will move this to a wiki page if it gets too big.

All Perl scripts fail with error message “Compilation failed in require at…*.pm did not return true at …”

Unable to install packages on Debian with error message “Perl may be unconfigured”

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