Kim Lab of Computational Evolutionary Biology
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Biology Department
School of Arts and Sciences
University of Pennsylvania
103I Lynch Laboratory
433 S University Avenue
Philadelphia, PA 19104 USA

off: (215) 746-5187
lab: (215) 898-8395
fax: (215) 898-8780

email: junhyong@sas.upenn.edu

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SoftwareQuestions

Question: Do we still have acroread installed? It stopped working for me after we upgraded my computer... do I need to change my path file? Thanks. -- JeanheeChung

Answer: You can use the X command 'xpdf' to display pdf files, making acroread obsolite. -- StephenFisher


Question: What's revision control?

Answer: See RevisionControl.


Question: Is there an easy way to manage multiple terminal sessions?

Answer: See UsingScreen.


Question: How do I find/replace a string in multiple text files?

Answer:

  • perl -pi -e 's/find/replace/g' *.txt

  • For a directory tree: find . -name '*.txt' | xargs perl -pi -e 's/find/replace/g'


Question: How do I change file extensions for a bunch of files (ex: aa.html to aa.shtml)?

Answer: In the directory: for i in *; do j=`echo $i | cut -d . -f 1`; mv $i "$j[new ext]"


Question: How do I count the number of files in a directory tree (use "-maxdepth 1" to limit directory depth)?

Answer: In the directory: find * -type f | wc -l