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Comments- Jitendra Narayan 4785 days ago
I like above mentioned cheat sheet, but this website link http://regexlib.com/CheatSheet.aspx?AspxAutoDetectCookieSupport=1 also provide nice and informative information at one place.
- Archana Malhotra 4785 days ago
Have a look at this cheat sheet http://www.cs.tut.fi/~jkorpela/perl/regexp.html
- Jitendra Narayan bookmarked Perl Module InstallationComments
- Rahul Nayak 3101 days ago
tar zxf Digest-SHA1-2.13.tar.gz cd Digest-SHA1-2.13 perl Makefile.PL make make test make install - BioStar 1285 days ago
To install BioPerl on a macOS system, you can follow these steps:
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Open the Terminal app on your macOS system.
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Install Homebrew if you haven't already installed it by entering the following command:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" -
Update Homebrew by entering the following command:
brew update -
Install Perl by entering the following command:
brew install perl -
Install cpanminus by entering the following command:
brew install cpanminus -
Install BioPerl by entering the following command:
cpanm BioPerl -
Verify the installation by running a BioPerl script or entering the following command to check the BioPerl version:
perl -MBio::Perl -e 'print "$Bio::Perl::VERSION\n"'
If there are any issues with the installation, you can try searching for solutions online or consulting the BioPerl documentation.
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- Archana Malhotra posted to the wire
- Jit published a blog post How to install Perl modules manually, using CPAN command, and other quick ways in the group Perl *PIPERsComments
- BioStar 1285 days ago
To install BioPerl on a macOS system, you can follow these steps:
-
-
Open the Terminal app on your macOS system.
-
Install Homebrew if you haven't already installed it by entering the following command:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" -
Update Homebrew by entering the following command:
brew update -
Install Perl by entering the following command:
brew install perl -
Install cpanminus by entering the following command:
brew install cpanminus -
Install BioPerl by entering the following command:
cpanm BioPerl -
Verify the installation by running a BioPerl script or entering the following command to check the BioPerl version:
perl -MBio::Perl -e 'print "$Bio::Perl::VERSION\n"'
If there are any issues with the installation, you can try searching for solutions online or consulting the BioPerl documentation.
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- BioStar 1279 days ago
Installing in CONDA env
You can check using
which perl- it should give you the perl that's located within your conda environment. In this case, it should install things into your conda-directory.When you install packages via cpan it will also print the folder perl is installing the package into.
If you want to be extra-sure, you can also install most Perl packages via conda. Replace the ':' by '-', lower-case everything, and add 'perl-' to the beginning. In your case,
conda install -c bioconda perl-lwp-simplethis will definitely install into conda.
- BioStar 1279 days ago
If using conda
conda create --name perlENV perl
conda activate perlENVconda install -c bioconda perl-bundle-bioperl
conda install -c bioconda perl-bioperl
- Archana Malhotra answered the question What a bioinformatician should must know ?
- Ankita is now a friend with Jitendra Narayan
- Jitendra Narayan is now a friend with Ankita
- Jit answered the question What a bioinformatician should must know ?
- Rahul Agarwal posted to the wire
- Rahul Agarwal commented on the blog Five unique traits of effective computational biologist
- Jitendra Narayan published a blog post Five unique traits of effective computational biologistComments
- Rahul Agarwal 4692 days ago
Corpas M, Fatumo S, Schneider R. (2012) How not to be a bioinformatician. Source Code Biol Med. 7(1):3. [link]
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Sandve GK, Nekrutenko A, Taylor J, Hovig E (2013) Ten Simple Rules for Reproducible Computational Research. PLoS Comput Biol9(10): e1003285. [link]
Bourne PE (2011) Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia. PLoS Comput Biol7(1): e1002001. [link]
Oshlack A (2013) A 10-step guide to party conversation for bioinformaticians. Genome Biology14:104 [link]
Via A, De Las Rivas J, Attwood TK, Landsman D, Brazas MD, et al. (2011) Ten Simple Rules for Developing a Short Bioinformatics Training Course. PLoS Comput Biol7(10): e1002245. [link]
Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Budd A, De Las
Rivas J, Dreyer J, Fernandes PL, van Gelder C, Jacob J, Jimenez RC, Loveland J,
Moran F, Mulder N, Nyrönen T, Rother K, Schneider MV, Attwood TK. (2013) Best practices
in bioinformatics training for life scientists. Brief Bioinform.14(5):528-37. [link]Slonim DK, Yanai I (2009) Getting Started in Gene Expression Microarray Analysis. PLoS Comput Biol5(10): e1000543. [link]
Logan DW, Sandal M, Gardner PP, Manske M, Bateman A (2010) Ten Simple Rules for Editing Wikipedia. PLoS Comput Biol6(9): e1000941. [link]
Prlić A, Procter JB (2012) Ten Simple Rules for the Open Development of Scientific Software. PLoS Comput Biol8(12): e1002802 [link]
Bernard V, Michaut M (2013) Explain Bioinformatics to Your Grandmother! PLoS Comput Biol9(10): e1003305. [link]
Noble WS (2009) A Quick Guide to Organizing Computational Biology Projects. PLoS Comput Biol5(7): e1000424. [link]
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Valencia A. (2002) Bioinformatics: biology by other means. Bioinformatics. 18(12):1551-2. [link]
Huttenhower C, Hofmann O (2010) A Quick Guide to Large-Scale Genomic Data Mining.PLoS Comput Biol6(5): e1000779. [link]
Dudley JT, Butte AJ (2009) A Quick Guide for Developing Effective Bioinformatics Programming Skills. PLoS Comput Biol5(12): e1000589. [link]
Bassi S (2007) A Primer on Python for Life Science Researchers. PLoS Comput Biol3(11): e199. [link]
Searls DB (2012) An Online Bioinformatics Curriculum. PLoS Comput Biol8(9): e1002632 [link]
Giddings MC (2008) On the Process of Becoming a Great Scientist. PLoS Comput Biol4(2): e33. [link]
Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C. (2013) The anatomy of successful computational biology software. Nat Biotechnol.31(10):894-7.
Nat. Biotech Editorial (2013) In need of an upgrade. Nat Biotechnol.31(10):857.
Li JW, Bolser D, Manske M, Giorgi FM, Vyahhi N, Usadel B, Clavijo BJ, Chan TF, Wong N, Zerbino D, Schneider MV. (2013) The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability. Brief Bioinform. 14(5):548-55.
- Radha Agarkar 4692 days ago
Recently published Nature commentary on "So you want to be a computational biologist?" by Nick Loman & Mick Watson give advice when starting out on computational projects. http://www.nature.com/nbt/journal/v31/n11/full/nbt.2740.html
- Archana Malhotra published a news post Bioinformatics: Introduction to PERL in the group Perl *PIPERsComments
- Jitendra Narayan 4783 days ago
Thanks Archana for such a useful links. I found this link useful as well for beginners, where user can find some of the free books.
