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linnarsson-lab / cytograph-dev

Algorithms for analysis of very large single-cell RNA-seq datasets
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graphviz cannot be installed in ubuntu #2

Closed gioelelm closed 6 years ago

gioelelm commented 7 years ago

Apparently Ubuntu has dropped a package that is a dependency for graphviz (and made it tricky to install since libgraphviz4 might break a preinstalled package libcdt5).

See more here: http://askubuntu.com/questions/418054/how-do-i-install-latest-graphviz

and this claims that it is solvable but it does not work for me: http://stackoverflow.com/questions/29630434/graphviz-installation-ubuntu-14-04

Any idea how to overcome this?

slinnarsson commented 7 years ago

Did you try the answer from SO?

Did you try the packages from here: http://www.graphviz.org/Download_linux_ubuntu.php ? The corresponding Mac packages work.

/Sten

-- Sten Linnarsson, PhD Professor of Molecular Systems Biology Karolinska Institutet Unit of Molecular Neurobiology Department of Medical Biochemistry and Biophysics Scheeles väg 1, 171 77 Stockholm, Sweden +46 8 52 48 75 77 (office) +46 70 399 32 06 (mobile)

On 30 Jan 2017, at 14:24, Gioele La Manno notifications@github.com wrote:

Apparently Ubuntu has dropped a package that is a dependency for graphviz (and made it tricky to install since libgraphviz4 might break a preinstalled package libcdt5).

See more here: http://stackoverflow.com/questions/29630434/graphviz-installation-ubuntu-14-04

Any idea how to overcome this?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

gioelelm commented 7 years ago

yes I downloaded from there tried with “dpkg/apt-get" and failed, then tried using “gdebi” and failed. The following stack overflow explains why: http://askubuntu.com/questions/418054/how-do-i-install-latest-graphviz http://askubuntu.com/questions/418054/how-do-i-install-latest-graphviz (I actually was linking to the wrong stack overflow page, edited )

/Gioele

On 30 Jan 2017, at 14:40, Sten Linnarsson notifications@github.com wrote:

Did you try the answer from SO?

Did you try the packages from here: http://www.graphviz.org/Download_linux_ubuntu.php ? The corresponding Mac packages work.

/Sten

-- Sten Linnarsson, PhD Professor of Molecular Systems Biology Karolinska Institutet Unit of Molecular Neurobiology Department of Medical Biochemistry and Biophysics Scheeles väg 1, 171 77 Stockholm, Sweden +46 8 52 48 75 77 (office) +46 70 399 32 06 (mobile)

On 30 Jan 2017, at 14:24, Gioele La Manno notifications@github.com wrote:

Apparently Ubuntu has dropped a package that is a dependency for graphviz (and made it tricky to install since libgraphviz4 might break a preinstalled package libcdt5).

See more here: http://stackoverflow.com/questions/29630434/graphviz-installation-ubuntu-14-04

Any idea how to overcome this?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/linnarsson-lab/cytograph/issues/2#issuecomment-276064817, or mute the thread https://github.com/notifications/unsubscribe-auth/AEA92nAfd4DNDC_y40sr8TKv048c9eFkks5rXehFgaJpZM4LxZXh.