Hi Christian,

This is an old Ubuntu bug. Please try to get rid of /use/bin/node and symlink /use/bin/nodejs to /usr/bin/node.

Hope this works for you, Bjoern On Jul 9, 2015 4:27 PM, "Christian Brenninkmeijer" < christian.brenninkmeijer@manchester.ac.uk> wrote:

Thank you for the excellent training session on using ipython in galaxy. http://gcc2015.tsl.ac.uk/training-day/#Galaxy_Interactive_Environments

However when I tried to repeat it on my desktop I had an error doing the step Change directory into: lib/galaxy/web/proxy/js/ $ cd lib/galaxy/web/proxy/js/ Then install the node proxy with “npm”: $ npm install .

I get: npm http GET https://registry.npmjs.org/sqlite3/3.0.2 npm http 304 https://registry.npmjs.org/sqlite3/3.0.2 npm http GET https://registry.npmjs.org/nan/1.3.0 npm http 304 https://registry.npmjs.org/nan/1.3.0

...

sqlite3@3.0.2 install

/home/christian/galaxy/lib/galaxy/web/proxy/js/node_modules/sqlite3

...

node-pre-gyp install --fallback-to-build

/usr/bin/env: node: No such file or directory npm WARN This failure might be due to the use of legacy binary "node" npm WARN For further explanations, please read /usr/share/doc/nodejs/README.Debian

npm ERR! weird error 127 npm ERR! not ok code 0

System Information: Galaxy master revision:6f53676f482634212bac512ec91dbf24e4afacff (also tried against today's dev)

OS: Distributor ID: Ubuntu Description: Ubuntu 14.04.2 LTS Release: 14.04 Codename: trusty

npm version: 1.3.10

Which is rather strange as these are all exactly the same as in the Virtual machine used.

Any one have any ideas?

Thanks in advance Christian

PS. Below is the content of: /usr/share/doc/nodejs/README.Debian nodejs for Debian =================

packaged modules

The global search path for modules is /usr/lib/nodejs

Future packages of node modules will use that directory, so it should be used wisely.

user modules

Node looks for modules in ./node_modules directory first; please read node#modules documentation carefully for more information.

Node does not look for modules in /usr/local/lib/node_modules, where npm put them. Please read npm-link(1) of npm package, to understand how to properly use npm-installed modules in a project.

Note that require.paths is not supported in future node versions. See also node(1) for more information about NODE_PATH.

nodejs command

The upstream name for the Node.js interpreter command is "node". In Debian the interpreter command has been changed to "nodejs".

This was done to prevent a namespace collision: other commands use the same name in their upstreams, such as ax25-node from the "node" package.

Scripts calling Node.js as a shell command must be changed to instead use the "nodejs" command.

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