<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36497?offset=40 https://bioinformaticsonline.com/blog/view/29479/how-to-install-perl-modules-on-mac-os-x-in-easy-steps Thu, 20 Oct 2016 07:26:29 -0500 https://bioinformaticsonline.com/blog/view/29479/how-to-install-perl-modules-on-mac-os-x-in-easy-steps <![CDATA[How to install Perl modules on Mac OS X in easy steps !!]]> Today at work, I learned how to install Perl modules using CPAN. It’s a lot easier than I thought.

You see, for the past couple of years, I’ve been a bit frustrated because OS X does not come with a whole lot of Perl modules pre-installed, and for all I googled, I couldn’t find an “idiot’s” guide for moderately-savvy-but-not-expert users like myself to install modules and dependencies on demand.

The only instructions I could find point to Fink, which basically installs modules in a path that isn’t included in the Perl @INC variable, meaning you have to manually specify the full path to the modules in every script — which is not a lot of fun if you’re developing on OS X and deploying on Red Hat, for instance.

Moreover, Fink doesn’t seem to make every module available, and it’s not very easy to determine which Fink package you need to install if you need a particular module.

So, with a script that called on several apparently unavailable modules, and a deadline looming, I finally decided to suck it up and figure out how to use CPAN to install them:

1) Make sure you have the Apple Developer Tools (XCode) installed.

These are on one of your install discs, or available as a huge but free download from the Apple Developer Connection [free registration required] or the Mac App Store. I thought I had them, but apparently when we upgraded that computer to Tiger, they went missing.

If you don’t have this stuff installed, your installation will fail with errors about unavailable commands.

1.5) Install Command Line Tools (Recent XCode versions only)

(Thank you to Tom Marchioro for informing me about this step.)

Older versions of XCode installed the command line tools (which are required to properly install CPAN modules) by default, but apparently newer ones do not. To check whether you have the command line tools already installed, run the following from the Terminal:

$ which make

This command checks the system for the “make” tool. If it spits out something like /usr/bin/make you’re golden and can skip ahead to Step 2. If you just get a new prompt and no output, you’ll need to install the tools:

  1. Launch XCode and bring up the Preferences panel.
  2. Click on the Downloads tab
  3. Click to install the Command Line Tools

If you like, you can run which make again to confirm that everything’s installed correctly.

2) Configure CPAN.

$ sudo perl -MCPAN -e shell

perl> o conf init

This will prompt you for some settings. You can accept the defaults for almost everything (just hit “return”). The two things you must fill in are the path to make (which should be /usr/bin/make or the value returned when you run which make from the command line) and your choice of CPAN mirrors (which you actually choose don’t really matter, but it won’t let you finish until you select at least one). If you use a proxy or a very restrictive firewall, you may have to configure those settings as well.

If you skip Step 2, you may get errors about make being unavailable.

3) Upgrade CPAN

$ sudo perl -MCPAN -e 'install Bundle::CPAN'

Don’t forget the sudo, or it’ll fail with permissions errors, probably when doing something relatively unimportant like installing man files.

This will spend a long time downloading, testing, and compiling various files and dependencies. Bear with it. It will prompt you a few times about dependencies. You probably want to enter “yes”. I agreed to everything it asked me, and everything turned out fine. YMMV of course. If everything installs properly, it’ll give you an “OK” at the end.

4) Install your modules. For each module….

$ sudo perl -MCPAN -e 'install Bundle::Name'

or

$ sudo perl -MCPAN -e 'install Module::Name'

This will install the module and its dependencies. Nice, eh? Again, don’t forget the sudo.

The first time you run this after upgrading CPAN, it may prompt you to configure again (see Step 2). If you accept its offer to try to configure itself automatically, it may just run through everything without a problem.

There are a couple of potential pitfalls with specific modules (such as theLWP::UserAgent / HEAD issue), but most have workarounds, and I haven’t run into anything that wasn’t easily recoverable.

And that’s it!

Did you find this useful? Is there anything I missed?

]]> Jit https://bioinformaticsonline.com/blog/view/37000/install-imagemagick-from-unix-source Wed, 20 Jun 2018 11:22:43 -0500 https://bioinformaticsonline.com/blog/view/37000/install-imagemagick-from-unix-source <![CDATA[Install ImageMagick from Unix Source]]> ImageMagick builds on a variety of Unix and Unix-like operating systems including Linux, Solaris, FreeBSD, Mac OS X, and others. A compiler is required and fortunately almost all modern Unix systems have one. Download ImageMagick.tar.gzfrom www.imagemagick.org or a mirrors and verify its message digest.

Unpack the distribution with this command:

tar xvzf ImageMagick.tar.gz

Next configure and compile ImageMagick. Note the pkg-config script is required so that ImageMagick can find certain optional delegate libraries on your system. To configure, type:

$ cd ImageMagick-7.0.8
$ ./configure
$ make

If ImageMagick configured and compiled without complaint, you are ready to install it on your system. Administrator privileges are required to install. To install, type

sudo make install

You may need to configure the dynamic linker run-time bindings:

sudo ldconfig /usr/local/lib

Finally, verify the ImageMagick install worked properly, type

/usr/local/bin/convert logo: logo.gif

For a more comprehensive test, run the ImageMagick validation suite. Ghostscript is a prerequisite, otherwise the EPS, PS, and PDF tests will fail.

make check

Congratulations, you have a working ImageMagick distribution and you are ready to use ImageMagick to convert, compose, or edit your images or perhaps you'll want to use one of the Application Program Interfaces for C, C++, Perl, and others.

The above instructions will satisfy a great number of ImageMagick users, but we suspect a few will have additional questions or problems to consider. For example, what does one do if ImageMagick fails to configure or compile? Or what if you don't have administrator privileges and what if you don't want to install ImageMagick in the default /../usr/local folder? You will find the answer to these questions, and more, in Advanced Unix Source Installation.

jitendra@jitendra-UNLOCK-INSTALL[Downloads] git clone https://github.com/ImageMagick/ImageMagick.git []
Cloning into 'ImageMagick'...
remote: Counting objects: 124593, done.
remote: Compressing objects: 100% (77/77), done.
remote: Total 124593 (delta 94), reused 94 (delta 64), pack-reused 124452
Receiving objects: 100% (124593/124593), 76.94 MiB | 24.07 MiB/s, done.
Resolving deltas: 100% (106498/106498), done.
Checking connectivity... done.
jitendra@jitendra-UNLOCK-INSTALL[Downloads] cd ImageMagick []
jitendra@jitendra-UNLOCK-INSTALL[ImageMagick] make []
make: *** No targets specified and no makefile found. Stop.
jitendra@jitendra-UNLOCK-INSTALL[ImageMagick] ./configure []
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configuring ImageMagick 7.0.8-3
checking whether build environment is sane... yes
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checking for jbig.h... yes
checking for jbg_dec_init in -ljbig... yes
checking if JBIG package is complete... yes
-------------------------------------------------------------
checking for JPEG...
checking jconfig.h usability... yes
checking jconfig.h presence... yes
checking for jconfig.h... yes
checking jerror.h usability... yes
checking jerror.h presence... yes
checking for jerror.h... yes
checking jmorecfg.h usability... yes
checking jmorecfg.h presence... yes
checking for jmorecfg.h... yes
checking jpeglib.h usability... yes
checking jpeglib.h presence... yes
checking for jpeglib.h... yes
checking for jpeg_read_header in -ljpeg... yes
checking for JPEG library is version 6b or later... yes
checking if JPEG package is complete... yes
-------------------------------------------------------------
checking for LCMS2... no

-------------------------------------------------------------
checking for LIBOPENJP2... no

-------------------------------------------------------------
checking for LQR... no

-------------------------------------------------------------
checking for LZMA... yes

-------------------------------------------------------------
checking for OPENEXR... no

-------------------------------------------------------------
checking for PANGO... yes

checking for PANGO... yes

-------------------------------------------------------------
checking for PNG... yes

-------------------------------------------------------------
checking for RAW_R... no

-------------------------------------------------------------
checking for TIFF...
checking tiff.h usability... yes
checking tiff.h presence... yes
checking for tiff.h... yes
checking tiffio.h usability... yes
checking tiffio.h presence... yes
checking for tiffio.h... yes
checking for TIFFOpen in -ltiff... yes
checking for TIFFClientOpen in -ltiff... yes
checking for TIFFIsByteSwapped in -ltiff... yes
checking for TIFFReadRGBATile in -ltiff... yes
checking for TIFFReadRGBAStrip in -ltiff... yes
checking if TIFF package is complete... yes
checking tiffconf.h usability... yes
checking tiffconf.h presence... yes
checking for tiffconf.h... yes
checking for TIFFIsCODECConfigured... yes
checking for TIFFMergeFieldInfo... yes
checking for TIFFIsBigEndian... yes
checking for TIFFReadEXIFDirectory... yes
checking for TIFFSetErrorHandlerExt... yes
checking for TIFFSetTagExtender... yes
checking for TIFFSetWarningHandlerExt... yes
checking for TIFFSwabArrayOfTriples... yes
-------------------------------------------------------------
checking for WEBP... no
checking for WEBPMUX... no

checking for WMF support ...
checking for libwmf/ipa.h... no
checking if WMF package is complete ... no
-------------------------------------------------------------
checking for XML... yes

-------------------------------------------------------------
checking for ImageMagick delegate programs...
checking for bpgdec... bpgdec
checking for bpgenc... bpgenc
checking for blender... blender
checking for xdg-open... /usr/bin/xdg-open
checking for ufraw-batch... ufraw-batch
checking for soffice... /usr/bin/soffice
checking for dvips... /usr/bin/dvips
checking for magick... magick
checking for magick... magick
checking for xterm... /usr/bin/xterm
checking for dot... /usr/bin/dot
checking for hp2xx... hp2xx
checking for html2ps... html2ps
checking for ilbmtoppm... /usr/bin/ilbmtoppm
checking for ppmtoilbm... /usr/bin/ppmtoilbm
checking for JxrDecApp... JxrDecApp
checking for JxrEncApp... JxrEncApp
checking for lepton... lepton
checking for lp... /usr/bin/lp
checking for lpr... /usr/bin/lpr
checking for gimp... /usr/bin/gimp
checking for magick... magick
checking for avconv... avconv
checking for ffmpeg... (cached) avconv
checking for avconv... avconv
checking for ffmpeg... (cached) avconv
checking for mrsidgeodecode... mrsidgeodecode
checking for mv... /bin/mv
checking for pcl6... pcl6
checking for gsx... no
checking for gsc... no
checking for gs... /usr/bin/gs
checking for rm... /bin/rm
checking for rsvg-convert... rsvg-convert
checking for inkscape... inkscape
checking for uniconvertor... uniconvertor
checking for dwebp... dwebp
checking for cwebp... cwebp
checking for curl... /usr/bin/curl
checking for gxps... gxps
checking for Apple fonts directory... not found!
checking for Dejavu fonts directory... not found!
checking for Ghostscript fonts directory... /usr/share/fonts/type1/gsfonts/
checking for URW-base35 fonts directory... not found!
checking for Windows fonts directory... not found!
checking for gnutar... no
checking for gtar... no
checking for tar... tar
checking for perl... perl
checking for rpmbuild... no
checking for rpm... no
checking for 7za... 7za
checking for zip... zip
-------------------------------------------------------------
checking for Ghostscript...
checking for Ghostscript version... 9.18
checking for gs color device... pnmraw
checking for gs alpha device... pngalpha
checking for gs CMYK device... pamcmyk32
checking for gs mono device... pbmraw
checking for gs PDF writing device... pdfwrite
checking for gs PS writing device... ps2write
checking for gs EPS writing device... eps2write
-------------------------------------------------------------
Update ImageMagick configuration
checking that generated files are newer than configure... done
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating common.shi
config.status: creating config/configure.xml
config.status: creating config/delegates.xml
config.status: creating config/ImageMagick.rdf
config.status: creating config/MagickCore.dox
config.status: creating config/MagickWand.dox
config.status: creating config/Magick++.dox
config.status: creating config/type-apple.xml
config.status: creating config/type-dejavu.xml
config.status: creating config/type-ghostscript.xml
config.status: creating config/type-urw-base35.xml
config.status: creating config/type-windows.xml
config.status: creating config/type.xml
config.status: creating ImageMagick.spec
config.status: creating Magick++/bin/Magick++-config
config.status: creating MagickCore/ImageMagick.pc
config.status: creating Magick++/lib/Magick++.pc
config.status: creating MagickCore/MagickCore-config
config.status: creating MagickCore/MagickCore.pc
config.status: creating MagickCore/version.h
config.status: creating Makefile
config.status: creating magick.sh
config.status: creating PerlMagick/check.sh
config.status: creating PerlMagick/default/Magick.pm
config.status: creating PerlMagick/Makefile.PL
config.status: creating PerlMagick/default/Makefile.PL
config.status: creating PerlMagick/quantum/Makefile.PL
config.status: creating PerlMagick/quantum/quantum.pm
config.status: creating PerlMagick/quantum/quantum.xs
config.status: creating PerlMagick/quantum/typemap
config.status: creating utilities/animate.1
config.status: creating utilities/compare.1
config.status: creating utilities/composite.1
config.status: creating utilities/conjure.1
config.status: creating utilities/convert.1
config.status: creating utilities/display.1
config.status: creating utilities/identify.1
config.status: creating utilities/ImageMagick.1
config.status: creating utilities/import.1
config.status: creating utilities/magick.1
config.status: creating utilities/magick-script.1
config.status: creating utilities/mogrify.1
config.status: creating utilities/montage.1
config.status: creating utilities/stream.1
config.status: creating MagickWand/MagickWand-config
config.status: creating MagickWand/MagickWand.pc
config.status: creating config/config.h
config.status: executing MagickCore/magick-baseconfig.h commands
config.status: creating MagickCore/magick-baseconfig.h - prefix MAGICKCORE for config/config.h defines
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing default commands
config.status: executing magick.sh.in commands
config.status: executing MagickCore-config.in commands
config.status: executing MagickWand-config.in commands
config.status: executing Magick++-config.in commands
config.status: executing PerlMagick/check.sh.in commands
configure:
==============================================================================
ImageMagick is configured as follows. Please verify that this configuration
matches your expectations.

Host system type: x86_64-pc-linux-gnu
Build system type: x86_64-pc-linux-gnu

Option Value
------------------------------------------------------------------------------
Shared libraries --enable-shared=yes yes
Static libraries --enable-static=yes yes
Build utilities --with-utilities=yes yes

 

/usr/bin/install -c -m 644 ./www/api/MagickCore/tab_l.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/tab_r.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/tabs.css /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/threshold_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/threshold_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/threshold_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/timer_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/timer_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/timer_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/token_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/token_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/token_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/transform_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/transform_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/transform_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/tree.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/type_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/type_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/type_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/utility_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/utility_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/utility_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/version_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/version_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/version_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/vms_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/vms_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/vms_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/widget_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/widget_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/widget_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xml-tree_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xml-tree_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xml-tree_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xwindow_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xwindow_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xwindow_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xwindow-private_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
/usr/bin/install -c -m 644 ./www/api/MagickCore/xwindow-private_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickCore
mkdir -p -- /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/animate_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/animate_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/animate_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/annotated.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/classes.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/compare_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/compare_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/compare_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/composite_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/composite_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/composite_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/conjure_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/conjure_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/conjure_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/convert_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/convert_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/convert_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/deprecate_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/deprecate_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/deprecate_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/dir_101f7ac0a894e32543a314e85b2e1524.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/dirs.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/display_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/display_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/display_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/doxygen.css /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/doxygen.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/drawing-wand_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/drawing-wand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/drawing-wand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/drawtest_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/files.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2blank.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2doc.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2folderclosed.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2folderopen.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2lastnode.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2link.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2mlastnode.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2mnode.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2node.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2plastnode.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2pnode.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/ftv2vertline.png /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/functions.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/functions_vars.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x61.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x62.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x63.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x64.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x65.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x67.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x69.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x6d.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x6e.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x6f.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x70.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x71.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x72.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x73.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x74.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x75.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x77.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_0x78.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_defs.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_enum.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_eval.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x63.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x64.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x67.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x69.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x6d.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x6e.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x70.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x72.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func_0x73.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_func.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_type.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/globals_vars.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/identify_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/identify_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/identify_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/import_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/import_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/import_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/index.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-image_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-image_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-image_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-property_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-property_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-property_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-wand_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick__wand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-wand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/MagickWand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick__wand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-wand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/MagickWand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-wand-private_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/magick-wand-private_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/main.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/mogrify_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/mogrify_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/mogrify_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/mogrify-private_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/mogrify-private_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/montage_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/montage_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/montage_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-iterator_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-iterator_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-iterator_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-wand_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-wand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-wand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-wand-private_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/pixel-wand-private_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/stream_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/stream_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/stream_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__CompositeOptions.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__DrawingWand.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__DrawVTable.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__MagickWand.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__PixelIterator.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/struct__PixelWand.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/studio_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/studio_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/tab_b.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/tab_l.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/tab_r.gif /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/tabs.css /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/tree.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/wand_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/wand_8h.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/wand_8h-source.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/usr/bin/install -c -m 644 ./www/api/MagickWand/wandtest_8c.html /usr/local/share/doc/ImageMagick-7/www/api/MagickWand
/bin/mkdir -p '/usr/local/share/doc/ImageMagick-7'
/usr/bin/install -c -m 644 LICENSE ChangeLog NEWS.txt '/usr/local/share/doc/ImageMagick-7'
/bin/mkdir -p '/usr/local/include/ImageMagick-7/Magick++'
/usr/bin/install -c -m 644 Magick++/lib/Magick++/Blob.h Magick++/lib/Magick++/CoderInfo.h Magick++/lib/Magick++/Color.h Magick++/lib/Magick++/Drawable.h Magick++/lib/Magick++/Exception.h Magick++/lib/Magick++/Functions.h Magick++/lib/Magick++/Geometry.h Magick++/lib/Magick++/Image.h Magick++/lib/Magick++/Include.h Magick++/lib/Magick++/Montage.h Magick++/lib/Magick++/Pixels.h Magick++/lib/Magick++/ResourceLimits.h Magick++/lib/Magick++/SecurityPolicy.h Magick++/lib/Magick++/Statistic.h Magick++/lib/Magick++/STL.h Magick++/lib/Magick++/TypeMetric.h '/usr/local/include/ImageMagick-7/Magick++'
/bin/mkdir -p '/usr/local/include/ImageMagick-7'
/usr/bin/install -c -m 644 Magick++/lib/Magick++.h '/usr/local/include/ImageMagick-7'
/bin/mkdir -p '/usr/local/share/man/man1'
/usr/bin/install -c -m 644 MagickCore/MagickCore-config.1 MagickWand/MagickWand-config.1 Magick++/bin/Magick++-config.1 utilities/ImageMagick.1 utilities/animate.1 utilities/compare.1 utilities/composite.1 utilities/conjure.1 utilities/convert.1 utilities/display.1 utilities/identify.1 utilities/import.1 utilities/magick.1 utilities/magick-script.1 utilities/mogrify.1 utilities/montage.1 utilities/stream.1 '/usr/local/share/man/man1'
/bin/mkdir -p '/usr/local/lib/pkgconfig'
/usr/bin/install -c -m 644 MagickCore/ImageMagick.pc MagickCore/MagickCore.pc MagickCore/ImageMagick-7.Q16HDRI.pc MagickCore/MagickCore-7.Q16HDRI.pc MagickWand/MagickWand.pc MagickWand/MagickWand-7.Q16HDRI.pc Magick++/lib/Magick++.pc Magick++/lib/Magick++-7.Q16HDRI.pc '/usr/local/lib/pkgconfig'
make[2]: Leaving directory '/home/jitendra/Downloads/ImageMagick'
make[1]: Leaving directory '/home/jitendra/Downloads/ImageMagick'
jitendra@jitendra-UNLOCK-INSTALL[ImageMagick] []

]]> Jit https://bioinformaticsonline.com/opportunity/view/871/postdoctoral-position-in-bioinformatics-sweden Sun, 14 Jul 2013 13:49:57 -0500 <![CDATA[Postdoctoral position in bioinformatics @ Sweden]]> Information about the department
The Department of Mathematical Sciences at Chalmers University of Technology and the University of Gothenburg has about 170 faculty and staff and is the largest department of mathematical sciences in the Nordic countries. The department belongs to both Chalmers University of Technology and the University of Gothenburg (for more information see http://www.chalmers.se/math/).

Job description
We are looking for a motivated, self-driven post-doctoral researcher to work with large-scale sequence data analysis. The position is for 24 months and located at Mathematical Statistics, Department of Mathematical Sciences in Erik Kristiansson’s research group. We are focused on methods development for and analysis of next generation DNA sequencing, in particular comparative metagenomics and gene expression analysis (RNA-seq). We have strong interdisciplinary profile and are actively collaborating with several experimental groups, especially within the environmental sciences, ecology, infectious diseases and cancer genomics. More information is available at http://bioinformatics.math.chalmers.se.

The Post-doctoral position is an appointment that offers an opportunity to qualify for further research positions within academia or industry. The majority of your working time is devoted to your own research, normally as a member of a research group. Included in your work is also to take part in supervision of Ph.D. students and M.Sc thesis students. Teaching of undergraduate students may also be included to a small extent.

The employment is limited to a maximum of 2 years (1+1).

Qualifications
The applicant should have Ph.D. degree preferably in bioinformatics, mathematics, statistics, computer science or equivalent by the start of the appointment. Experience from analysis of large-scale data, in particular from next generation DNA sequencing, is highly valued. The applicant should also be proficient in programming (e.g. Python/Java/C) and comfortable with Unix/Linux systems. Interaction with experimental biologists is central and good collaborative skills are therefore important. Fluency in written and spoken English is a strong requirement. As a post-doctoral researcher you are expected to work independently and to be able to supervise/co-supervise PhD and Master’s students.

Application procedure
The application should be marked with Ref 20130126 and written in English. The application should be sent electronically via Chalmers webpage.

Application deadline: September 8, 2013.

For questions, please contact:
Ass prof. Erik Kristiansson, Matematiska Vetenskaper, erik.kristiansson@chalmers.se, +46 31-772 3521, +46 70-5259751.

Chalmers continuously strive to be an attractive employer. Equality and diversity are substantial foundations in all activities at Chalmers.

]]> https://bioinformaticsonline.com/news/view/14186/pybedtools Wed, 20 Aug 2014 01:03:41 -0500 https://bioinformaticsonline.com/news/view/14186/pybedtools <![CDATA[pybedtools]]> pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs (https://github.com/arq5x/bedtools), which are widely used for genomic interval manipulation or "genome algebra". pybedtools extends BEDTools by offering feature-level manipulations from with Python. See full online documentation, including installation instructions, at http://pythonhosted.org/pybedtools/.

More at http://pythonhosted.org/pybedtools/

A powerful toolset for genome arithmetic.http://code.google.com/p/bedtools/

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/22961/bioscripts Sun, 28 Jun 2015 07:46:14 -0500 https://bioinformaticsonline.com/bookmarks/view/22961/bioscripts <![CDATA[BioScripts]]> You are requested to please bookmark collection of bioinformatics tools, scripts, codes that can be pieced together in a very easy and flexible manner to perform both simple and complex bioinformatics tasks.

The next-generation sequencing included whole genome sequencing(WGS), transcriptome sequencing (whole cDNA sequencing, RNA-seq), digital gene expression sequencing (Tag-Seq), ChIP-Seq, and so on. And there are many sequencing platform to generate sequece, as well know Sanger/ABi(the frist generation), Solexa/illumina, SOLiD/ABi, 454/Roche. But thier sequence format is different, also they have different error type. High quality data is very important for further analysis or data mining. There are many pipeline for raw sequence quality analysis and control with few of process for reporting reads quality statistical details, trimming, filtering, and error correction. Please bookmarks them for the benefits of bioinformatics community.

https://code.google.com/p/biowiki/

https://code.google.com/p/ngs-pipeline/source/browse/#svn%2Ftrunk

NGSand Perl scripts https://code.google.com/hosting/search?q=NGS+perl&projectsearch=Search+projects

NGS and Python scripts https://code.google.com/hosting/search?q=NGS+Python&projectsearch=Search+projects

Address of the bookmark: https://code.google.com/hosting/search?q=bioinformatics&sa=Search

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/33398/tiny-python36-notebook Sat, 03 Jun 2017 03:16:28 -0500 https://bioinformaticsonline.com/bookmarks/view/33398/tiny-python36-notebook <![CDATA[Tiny Python3.6 Notebook]]> This is not so much an instructional manual, but rather notes, tables, and examples for Python syntax. It was created by the author as an additional resource during training, meant to be distributed as a physical notebook. Participants (who favor the physical characteristics of dead tree material) could add their own notes, thoughts, and have a valuable reference of curated examples.

Address of the bookmark: https://github.com/mattharrison/Tiny-Python-3.6-Notebook/blob/master/python.rst

]]> Neel https://bioinformaticsonline.com/bookmarks/view/40221/dash-a-web-application-framework-that-provides-pure-python-abstraction-around-html-css-and-javascript Tue, 05 Nov 2019 06:39:48 -0600 https://bioinformaticsonline.com/bookmarks/view/40221/dash-a-web-application-framework-that-provides-pure-python-abstraction-around-html-css-and-javascript <![CDATA[Dash: a web application framework that provides pure Python abstraction around HTML, CSS, and JavaScript.]]> Dash is a web application framework that provides pure Python abstraction around HTML, CSS, and JavaScript.

Dash Bio is a suite of bioinformatics components that make it simpler to analyze and visualize bioinformatics data and interact with them in a Dash application.

The source can be found on GitHub at plotly/dash-bio.

These docs are using Dash Bio version 0.1.4.

Address of the bookmark: https://dash.plot.ly/dash-bio

]]> Jit https://bioinformaticsonline.com/opportunity/view/41043/postdoctoral-scientist-genome-analytics-genome-bioinformatics-mf Sun, 16 Feb 2020 02:57:40 -0600 <![CDATA[Postdoctoral scientist genome analytics/ genome bioinformatics (m/f/*)]]> https://www.uksh.de/jobs/Stellenangebote-nr-20190570-p-8.html
Your profile:
Degree in bioinformatics, biostatistics, or equivalent
Experience in the processing and analysis of large-scale genomics data using compute clusters / high-performance computing
Strong competence in working in Unix/Linux environments (shell)
Strong programming skills (in particular: Python, R, Perl)
Experience with using git and snakemake
Fluent English language skills, both spoken and written
Strong communication skills and motivation to work in a young, interdisciplinary, dynamic team

Additional Information:

If you have any questions about scientific aspects of this position, please contact Prof. Lars Bertram, head of LIGA (lars.bertram@uni-luebeck.de).

Please contact Ms. Anna Wolbert for further questions about administrative details (recruiting@uksh.de).

Weitere Informationen erhalten Sie auch unter www.uksh.de/karriere.

Wir freuen uns auf Ihre Bewerbung bis zum 15.03.2020 unter Angabe unserer Ausschreibungsnummer 20190570.119.CL.

]]> https://bioinformaticsonline.com/blog/view/44633/learn-python-with-example Tue, 06 Aug 2024 23:51:51 -0500 https://bioinformaticsonline.com/blog/view/44633/learn-python-with-example <![CDATA[Learn python with example]]>

There are over 21 unique Python project walkthroughs in this content that range from beginner to advanced. See below for the timestamps for these projects:

00:00:00 | How To Navigate These Projects
---
00:01:46 | #1 - Quiz Game (Easy)
Code: https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/quiz_game.py 
---
00:22:00 | #2 - Number Guessing Game (Easy)
Code: https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/number_guesser.py 
---
00:39:49 | #3 - Rock, Paper, Scissors (Easy)
Code: https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/rock_paper_scissors.py 
---
00:54:40 | #4 - Choose Your Own Adventure Game (Easy)
Code: https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/choose_your_own_adventure.py 
---
01:06:47 | #5 - Password Manager (Medium)
Code: https://github.com/techwithtim/5-Python-Projects-For-Beginners/ 
Fernet Cryptography Documentation: https://cryptography.io/en/latest/fernet/ 
---
01:37:37 | #6 - PIG (Medium)
Code: https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project1.py 
---
01:59:07 | #7 - Madlibs Generator (Medium)
Code: https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project2.py 
---
02:15:04 | #8 - Timed Math Challenge (Medium)
Code: https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project3.py 
---
02:28:02 | #9 - Slot Machine (Medium)
Code: https://github.com/techwithtim/Python-Slot-Machine 
---
03:20:43 | #10 - Turtle Racing (Medium)
Code: https://github.com/techwithtim/Turtle-Racing-V2 
Turtle Docs: https://docs.python.org/3/library/turtle.html 
---
04:13:09 | #11 - WPM Typing Test (Medium)
Code: https://github.com/techwithtim/WPM_Typing_Test 
Curses Docs: https://docs.python.org/3/howto/curses.html 
05:09:43 | #12 - Alarm Clock (Easy)
Python Project Idea Blog: https://hackr.io/blog/python-projects 
Sound Effects: https://www.fesliyanstudios.com/royalty-free-sound-effects-download/alarm-203 
---
05:22:07 | #13 - Password Generator (Easy)
Python Project Idea Blog: https://hackr.io/blog/python-projects 
---
05:39:16 | #14 - Shortest Path Finder (Advanced)
Code: https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/path-finder.py 
---
06:14:53 | #15 - NBA Stats & Current Scores (Medium)
Code: https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/nba-scores.py 
---
06:38:22 | #16 - Currency Converter (Medium)
Code: https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/currency-converter.py 
API: https://free.currencyconverterapi.com/
---
06:58:51 | #17 - YouTube Video Downloader (Medium)
Code:  https://github.com/techwithtim/Python-Beginner-Automation-Projects/blob/main/youtube.py 
---
07:09:50 | #18 - Automated File Backup (Medium)
Code: https://github.com/techwithtim/Python-Beginner-Automation-Projects/blob/main/backup.py 
---
07:21:18 | #19 - Mastermind/4 Color Match (Advanced)
---
07:48:20 | #20 - Aim Trainer (Advanced)
Code: https://github.com/techwithtim/Python-Aim-Trainer 
---
08:39:20 | #21 - Advanced Python Scripting (Advanced)
Code: https://github.com/techwithtim/Python-Scripting-Project 

]]> BioStar https://bioinformaticsonline.com/pages/view/36502/creating-conda-environment-for-python27 Mon, 07 May 2018 08:56:52 -0500 https://bioinformaticsonline.com/pages/view/36502/creating-conda-environment-for-python27 <![CDATA[Creating conda environment for python2.7]]> TIP: By default, environments are installed into the envs directory in your conda directory. Run conda create --help for information on specifying a different path.

Use the Terminal or an Anaconda Prompt for the following steps.

  1. To create an environment:

    conda create --name myenv

    NOTE: Replace myenv with the environment name.

  2. When conda asks you to proceed, type y:

    proceed ([y]/n)?

This creates the myenv environment in /envs/. This environment uses the same version of Python that you are currently using, because you did not specify a version.

To create an environment with a specific version of Python:

conda create -n myenv python=3.4

To create an environment with a specific package:

conda create -n myenv scipy

OR:

conda create -n myenv python
conda install -n myenv scipy

To create an environment with a specific version of a package:

conda create -n myenv scipy=0.15.0

OR:

conda create -n myenv python
conda install -n myenv scipy=0.15.0

To create an environment with a specific version of Python and multiple packages:

conda create -n myenv python=3.4 scipy=0.15.0 astroid babel

TIP: Install all the programs that you want in this environment at the same time. Installing 1 program at a time can lead to dependency conflicts.

To automatically install pip or another program every time a new environment is created, add the default programs to the create_default_packages section of your .condarc configuration file. The default packages are installed every time you create a new environment. If you do not want the default packages installed in a particular environment, use the --no-default-packages flag:

conda create --no-default-packages -n myenv python

TIP: You can add much more to the conda create command. For details, run conda create --help.

➜ redundans git:(master) ✗ conda create --name py27 python=2.7
Solving environment: done


==> WARNING: A newer version of conda exists. <==
current version: 4.5.0
latest version: 4.5.2

Please update conda by running

$ conda update -n base conda

 

## Package Plan ##

environment location: /home/urbe/anaconda3/envs/py27

added / updated specs:
- python=2.7


The following packages will be downloaded:

package | build
---------------------------|-----------------
wheel-0.31.0 | py27_0 61 KB
python-2.7.15 | h1571d57_0 12.1 MB
certifi-2018.4.16 | py27_0 142 KB
sqlite-3.23.1 | he433501_0 1.5 MB
setuptools-39.1.0 | py27_0 582 KB
openssl-1.0.2o | h20670df_0 3.4 MB
pip-10.0.1 | py27_0 1.7 MB
ca-certificates-2018.03.07 | 0 124 KB
------------------------------------------------------------
Total: 19.6 MB

The following NEW packages will be INSTALLED:

ca-certificates: 2018.03.07-0
certifi: 2018.4.16-py27_0
libedit: 3.1-heed3624_0
libffi: 3.2.1-hd88cf55_4
libgcc-ng: 7.2.0-hdf63c60_3
libstdcxx-ng: 7.2.0-hdf63c60_3
ncurses: 6.0-h9df7e31_2
openssl: 1.0.2o-h20670df_0
pip: 10.0.1-py27_0
python: 2.7.15-h1571d57_0
readline: 7.0-ha6073c6_4
setuptools: 39.1.0-py27_0
sqlite: 3.23.1-he433501_0
tk: 8.6.7-hc745277_3
wheel: 0.31.0-py27_0
zlib: 1.2.11-ha838bed_2

Proceed ([y]/n)? y


Downloading and Extracting Packages
wheel 0.31.0: #################################################################################################################################################################################################### | 100%
python 2.7.15: ################################################################################################################################################################################################### | 100%
certifi 2018.4.16: ############################################################################################################################################################################################### | 100%
sqlite 3.23.1: ################################################################################################################################################################################################### | 100%
setuptools 39.1.0: ############################################################################################################################################################################################### | 100%
openssl 1.0.2o: ################################################################################################################################################################################################## | 100%
pip 10.0.1: ###################################################################################################################################################################################################### | 100%
ca-certificates 2018.03.07: ###################################################################################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use:
# > source activate py27
#
# To deactivate an active environment, use:
# > source deactivate
#

➜ redundans git:(master) ✗ source activate py27

]]> Jit