BioInfo@TO.CNR Dev zone
http://devbioinfo.to.cnr.it/
2024-03-28T15:59:35+0100
BioInfo@TO.CNR Dev zone
http://devbioinfo.to.cnr.it/
http://devbioinfo.to.cnr.it/lib/tpl/drupal-garland-blue/images/favicon.ico
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2017-01-20T17:26:47+0100
giancarlo (giancarlo@undisclosed.example.com)
start
http://devbioinfo.to.cnr.it/doku.php?id=start&rev=1484929607&do=diff
Bioinformatics project at CNR Piedmont Research Area.
The open-source community helped us to build on our project and this site is our thanks, of course at disposal of the open-source community.
Infrastructure for bioinformatics applications
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2017-01-20T17:26:30+0100
giancarlo (giancarlo@undisclosed.example.com)
rxr:start
http://devbioinfo.to.cnr.it/doku.php?id=rxr:start&rev=1484929590&do=diff
Virtual server for applications - Ubuntu 16.04 - RachaelXReloaded
* Install base system
* Install Blast+
* R, RStudio server
* Bowtie and Bowtie2
* Samtools, Tophat and Tophat2
* BWA
* Bioperl
* Mira
* Trinity
* RSEM
* AllPaths-LG
* More tools
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2017-01-20T17:25:58+0100
giancarlo (giancarlo@undisclosed.example.com)
rxr:moretools - created
http://devbioinfo.to.cnr.it/doku.php?id=rxr:moretools&rev=1484929558&do=diff
More tools
* Insync
# apt-key adv --keyserver keyserver.ubuntu.com --recv-keys ACCAF35C
# nano -w /etc/apt/sources.list.d/insync.list
+deb http://apt.insynchq.com/ubuntu xenial non-free contrib
# apt-get update
# apt-get install insync-headless
$ insync-headless --version
1.3.14.36131
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2017-01-20T12:53:14+0100
giancarlo (giancarlo@undisclosed.example.com)
rxr:allpathlg - created
http://devbioinfo.to.cnr.it/doku.php?id=rxr:allpathlg&rev=1484913194&do=diff
AllPaths-LG
* Download
# wget ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/LATEST_VERSION.tar.gz
# tar xvf LATEST_VERSION.tar.gz
* add gcc/g++ version 4.9
# apt-get install g++-4.9
# update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 10
# update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5 20
# update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.9 10
# update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-5 20
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2017-01-16T11:38:52+0100
giancarlo (giancarlo@undisclosed.example.com)
rxr:trinity
http://devbioinfo.to.cnr.it/doku.php?id=rxr:trinity&rev=1484563132&do=diff
Trinity
* Download and compile
# wget https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.3.2.tar.gz
# tar xzf Trinity-v2.3.2.tar.gz
# cd trinityrnaseq-Trinity-v2.3.2/
# make
...
Performing Unit Tests of Build
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
JellyFish: has been Installed Properly
Inchworm: has been Installed Properly
Chrysalis: has been Installed Properly
QuantifyGraph: has been Installed Properly
GraphFromFa…
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2017-01-16T11:38:34+0100
giancarlo (giancarlo@undisclosed.example.com)
rxr:rsem - created
http://devbioinfo.to.cnr.it/doku.php?id=rxr:rsem&rev=1484563114&do=diff
RSEM
* Download and Install RSEM
wget https://github.com/deweylab/RSEM/archive/v1.3.0.tar.gz
tar -xvzf v1.3.0.tar.gz
cd RSEM-1.3.0
make
make install
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2015-01-15T13:42:16+0100
giancarlo (giancarlo@undisclosed.example.com)
logo_h51.png - created
http://devbioinfo.to.cnr.it/doku.php?image=logo_h51.png&ns=&rev=1421325736&tab_details=history&mediado=diff&do=media
<img src="http://devbioinfo.to.cnr.it/lib/exe/fetch.php?w=144&h=51&t=1421325736&tok=017bce&media=logo_h51.png" alt="logo_h51.png" />
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2015-01-15T13:39:12+0100
giancarlo (giancarlo@undisclosed.example.com)
ircres_h51.png - created
http://devbioinfo.to.cnr.it/doku.php?image=ircres_h51.png&ns=&rev=1421325552&tab_details=history&mediado=diff&do=media
<img src="http://devbioinfo.to.cnr.it/lib/exe/fetch.php?w=123&h=51&t=1421325552&tok=dbdca5&media=ircres_h51.png" alt="ircres_h51.png" />
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2013-04-18T10:55:23+0100
giancarlo (giancarlo@undisclosed.example.com)
isla:screenshot_from_2013-04-18_09_38_25.png - created
http://devbioinfo.to.cnr.it/doku.php?image=isla%3Ascreenshot_from_2013-04-18_09_38_25.png&ns=isla&rev=1366275323&tab_details=history&mediado=diff&do=media
<img src="http://devbioinfo.to.cnr.it/lib/exe/fetch.php?w=500&h=264&t=1366275323&tok=5c0561&media=isla:screenshot_from_2013-04-18_09_38_25.png" alt="isla:screenshot_from_2013-04-18_09_38_25.png" />
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2013-04-18T10:53:42+0100
giancarlo (giancarlo@undisclosed.example.com)
isla:screenshot_from_2013-04-18_09_38_02.png - created
http://devbioinfo.to.cnr.it/doku.php?image=isla%3Ascreenshot_from_2013-04-18_09_38_02.png&ns=isla&rev=1366275222&tab_details=history&mediado=diff&do=media
<img src="http://devbioinfo.to.cnr.it/lib/exe/fetch.php?w=500&h=344&t=1366275222&tok=78f349&media=isla:screenshot_from_2013-04-18_09_38_02.png" alt="isla:screenshot_from_2013-04-18_09_38_02.png" />
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2013-04-18T10:50:00+0100
giancarlo (giancarlo@undisclosed.example.com)
isla:screenshot_from_2013-04-18_09_33_54.png - created
http://devbioinfo.to.cnr.it/doku.php?image=isla%3Ascreenshot_from_2013-04-18_09_33_54.png&ns=isla&rev=1366275000&tab_details=history&mediado=diff&do=media
<img src="http://devbioinfo.to.cnr.it/lib/exe/fetch.php?w=500&h=239&t=1366275000&tok=36881d&media=isla:screenshot_from_2013-04-18_09_33_54.png" alt="isla:screenshot_from_2013-04-18_09_33_54.png" />
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2013-04-18T10:47:02+0100
giancarlo (giancarlo@undisclosed.example.com)
isla:screenshot_from_2013-04-18_09_29_31.png - created
http://devbioinfo.to.cnr.it/doku.php?image=isla%3Ascreenshot_from_2013-04-18_09_29_31.png&ns=isla&rev=1366274822&tab_details=history&mediado=diff&do=media
<img src="http://devbioinfo.to.cnr.it/lib/exe/fetch.php?w=500&h=75&t=1366274822&tok=97ae93&media=isla:screenshot_from_2013-04-18_09_29_31.png" alt="isla:screenshot_from_2013-04-18_09_29_31.png" />
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2013-04-12T11:50:52+0100
giancarlo (giancarlo@undisclosed.example.com)
isla:screenshot_from_2013-04-12_11_50_26.png - created
http://devbioinfo.to.cnr.it/doku.php?image=isla%3Ascreenshot_from_2013-04-12_11_50_26.png&ns=isla&rev=1365760252&tab_details=history&mediado=diff&do=media
<img src="http://devbioinfo.to.cnr.it/lib/exe/fetch.php?w=500&h=368&t=1365760252&tok=204ba4&media=isla:screenshot_from_2013-04-12_11_50_26.png" alt="isla:screenshot_from_2013-04-12_11_50_26.png" />
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2013-04-12T11:16:43+0100
giancarlo (giancarlo@undisclosed.example.com)
isla:screenshot_from_2013-04-12_11_16_30.png - created
http://devbioinfo.to.cnr.it/doku.php?image=isla%3Ascreenshot_from_2013-04-12_11_16_30.png&ns=isla&rev=1365758203&tab_details=history&mediado=diff&do=media
<img src="http://devbioinfo.to.cnr.it/lib/exe/fetch.php?w=500&h=213&t=1365758203&tok=509edc&media=isla:screenshot_from_2013-04-12_11_16_30.png" alt="isla:screenshot_from_2013-04-12_11_16_30.png" />
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2013-04-12T11:15:03+0100
giancarlo (giancarlo@undisclosed.example.com)
isla:screenshot_from_2013-04-12_11_14_34.png - created
http://devbioinfo.to.cnr.it/doku.php?image=isla%3Ascreenshot_from_2013-04-12_11_14_34.png&ns=isla&rev=1365758103&tab_details=history&mediado=diff&do=media
<img src="http://devbioinfo.to.cnr.it/lib/exe/fetch.php?w=500&h=361&t=1365758103&tok=42dc99&media=isla:screenshot_from_2013-04-12_11_14_34.png" alt="isla:screenshot_from_2013-04-12_11_14_34.png" />
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2013-04-12T10:44:13+0100
giancarlo (giancarlo@undisclosed.example.com)
isla:screenshot_from_2013-04-12_10_43_38.png - created
http://devbioinfo.to.cnr.it/doku.php?image=isla%3Ascreenshot_from_2013-04-12_10_43_38.png&ns=isla&rev=1365756253&tab_details=history&mediado=diff&do=media
<img src="http://devbioinfo.to.cnr.it/lib/exe/fetch.php?w=500&h=140&t=1365756253&tok=5a70a1&media=isla:screenshot_from_2013-04-12_10_43_38.png" alt="isla:screenshot_from_2013-04-12_10_43_38.png" />
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2013-04-11T16:11:39+0100
giancarlo (giancarlo@undisclosed.example.com)
isla:screenshot_from_2013-04-11_16_10_41.png - created
http://devbioinfo.to.cnr.it/doku.php?image=isla%3Ascreenshot_from_2013-04-11_16_10_41.png&ns=isla&rev=1365689499&tab_details=history&mediado=diff&do=media
<img src="http://devbioinfo.to.cnr.it/lib/exe/fetch.php?w=500&h=284&t=1365689499&tok=8e54f7&media=isla:screenshot_from_2013-04-11_16_10_41.png" alt="isla:screenshot_from_2013-04-11_16_10_41.png" />
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2013-04-10T16:00:37+0100
giancarlo (giancarlo@undisclosed.example.com)
isla:screenshot_from_2013-04-10_15_25_57.png - created
http://devbioinfo.to.cnr.it/doku.php?image=isla%3Ascreenshot_from_2013-04-10_15_25_57.png&ns=isla&rev=1365602437&tab_details=history&mediado=diff&do=media
<img src="http://devbioinfo.to.cnr.it/lib/exe/fetch.php?w=499&h=308&t=1365602437&tok=33a905&media=isla:screenshot_from_2013-04-10_15_25_57.png" alt="isla:screenshot_from_2013-04-10_15_25_57.png" />
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2013-04-10T15:58:48+0100
giancarlo (giancarlo@undisclosed.example.com)
isla:screenshot_from_2013-04-10_15_24_50.png - created
http://devbioinfo.to.cnr.it/doku.php?image=isla%3Ascreenshot_from_2013-04-10_15_24_50.png&ns=isla&rev=1365602328&tab_details=history&mediado=diff&do=media
<img src="http://devbioinfo.to.cnr.it/lib/exe/fetch.php?w=500&h=274&t=1365602328&tok=5c910c&media=isla:screenshot_from_2013-04-10_15_24_50.png" alt="isla:screenshot_from_2013-04-10_15_24_50.png" />
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2013-04-10T12:45:44+0100
giancarlo (giancarlo@undisclosed.example.com)
isla:screenshot_from_2013-04-10_12_40_01.png - created
http://devbioinfo.to.cnr.it/doku.php?image=isla%3Ascreenshot_from_2013-04-10_12_40_01.png&ns=isla&rev=1365590744&tab_details=history&mediado=diff&do=media
<img src="http://devbioinfo.to.cnr.it/lib/exe/fetch.php?w=461&h=500&t=1365590744&tok=d8b074&media=isla:screenshot_from_2013-04-10_12_40_01.png" alt="isla:screenshot_from_2013-04-10_12_40_01.png" />