Hi David, To address the download of the compiled program, we suggest that you double check the read and executable permissions. It seems simple, but is easy to miss and worth a check and will keep things simple. Perhaps this will solve the issue with the unusual tool display/usability (color coding may be a clue that permissions are set differently, especially when the color is different from other functioning executables).
If you still require a recompile, the environment needs to be set up correctly from the top. To do this, see the general help here: http://genomewiki.cse.ucsc.edu/index.php/The_source_tree Specifically, follow the link to http://genome.ucsc.edu/admin/jk-install.html (The last step #8 is where you would compile utilities in the tree). For the utility that you are interested in, once compiled, please note that test sets along with expected results are included in the same directory. (BTW - Stringify is utility that nearly everything in our build system needs early. It makes itself first when all of the basic building directions are followed and the environments setup completes correctly.) If you need more help with compiling, please send more information about your machine, environment and OS and we can offer detailed help. With all of that said (and good to know anyway if you are using the kent source tree for more than one use), for this particular task, there are other tools that may be better solutions for your data analysis project. So, the recommendation for the pslReps vs pslCDna question is to instead use one of the many good specialized (and free) short-read aligners that are available such as MAQ, Bowtie, etc. A google search with the string "short read alignment" provides several links to tools to choose from. Some experimentation is probably necessary to determine which is the best fit for your project data, input volume, and computational resources. We hope this helps to resolve the problems you experienced, but please let us know if you need more advice, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "David G. Drewry,III (NSTD)" <[email protected]> wrote: > From: "David G. Drewry,III (NSTD)" <[email protected]> > To: [email protected] > Sent: Tuesday, January 12, 2010 9:33:33 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] pslCDna Filter > > I am an undergraduate student working on a gene expression project and > am using the Blat software package to map reads from both 454 and > Illumina systems. We are currently using pslReps to filter our data, > however we believe that the pslCDna filter would be better suited for > our application. When we download the executable from > http://hgdownload.cse.ucsc.edu/admin/exe/ it will not run. When > viewing it in the terminal, it appears black, whereas other > executables such as Blat and the pslReps filter appear green. We > tried downloading the filter from source > (http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/pslCDnaFilter/) but > when we try to build by typing make we get the following error: > > > > [drewr...@feldmab1-ws1 pslCDnaFilter]$ make > > > > > > echo '/* GENERATED CODE, DO NOT EDIT */' > usage.msg.tmp > > > > > > /home/drewrdg2/bin//stringify usage.txt >> usage.msg.tmp > > > > > > /bin/sh: /home/drewrdg2/bin//stringify: No such file or directory > > > > > > make: *** [usage.msg] Error 127 > > > > Is there something that we are simply overlooking when we install the > executable or is there a problem with the executable? Also, do you > know the fundamental differences between the two filters and if it is > adequate to use the pslReps filter for cDNA data? > > > > Thanks, > > > David > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
