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error installing msa #1

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ialarmedalien opened this issue Apr 25, 2016 · 5 comments
Open

error installing msa #1

ialarmedalien opened this issue Apr 25, 2016 · 5 comments

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@ialarmedalien
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npm 2.14.12
biojs2galaxy 0.0.7

I've installed biojs2galaxy globally, and am now trying to install the MSA module, but getting the following errors:

$ biojs2galaxy -o config/plugins/visualizations/ msa
#tmpdir:  /tmp/tmp-71377s4wj1s0
[ 'galaxy-biojs', 'galaxy-vis' ]
biojs-vis-sequence: installing
drawrnajs: installing
exelixis-galaxy: installing
msa: installing
workmen info # pkgs 4
main info exelixis-galaxy: finished -> mako
brows debug exelixis-galaxy: starting browserify
brows debug exelixis-galaxy: browserify basedir:/tmp/tmp-71377s4wj1s0/node_modules/exelixis-galaxy
brows debug exelixis-galaxy: exposing:  lib/index.js
brows debug exelixis-galaxy: starting resourcify
brows debug exelixis-galaxy: resourcify:  /build/exelixis.js
brows debug exelixis-galaxy: starting resourcify
brows debug exelixis-galaxy: starting configy
stderr:  npm WARN unmet dependency /tmp/tmp-71377s4wj1s0/node_modules/msa/node_modules/biojs-io-fasta/node_modules/biojs-io-parser requires xhr@'^2.0.1' but will load
npm WARN unmet dependency /tmp/tmp-71377s4wj1s0/node_modules/msa/node_modules/xhr,
npm WARN unmet dependency which is version 1.17.1
npm WARN unmet dependency /tmp/tmp-71377s4wj1s0/node_modules/msa/node_modules/biojs-io-gff/node_modules/biojs-io-parser requires xhr@'^2.0.1' but will load
npm WARN unmet dependency /tmp/tmp-71377s4wj1s0/node_modules/msa/node_modules/xhr,
npm WARN unmet dependency which is version 1.17.1

main info drawrnajs: finished -> mako
brows debug drawrnajs: starting browserify
brows debug drawrnajs: browserify basedir:/tmp/tmp-71377s4wj1s0/node_modules/drawrnajs
brows debug drawrnajs: exposing:  src/drawrna.js
brows debug drawrnajs: starting resourcify
brows debug drawrnajs: resourcify:  /build/drawrnajs.js
brows debug drawrnajs: starting resourcify
brows debug drawrnajs: resourcify:  /style/bootstrap.css
brows debug drawrnajs: resourcify:  /style/spectrum.css
brows debug drawrnajs: resourcify:  /style/style.css
brows debug drawrnajs: starting configy
main info biojs-vis-sequence: finished -> mako
brows debug biojs-vis-sequence: starting browserify
brows debug biojs-vis-sequence: browserify basedir:/tmp/tmp-71377s4wj1s0/node_modules/biojs-vis-sequence
brows debug biojs-vis-sequence: exposing:  lib/index.js
brows debug biojs-vis-sequence: browserify require biojs-io-fasta
brows debug biojs-vis-sequence: starting resourcify
brows debug biojs-vis-sequence: resourcify:  http://code.jquery.com/jquery-1.11.0.min.js
brows debug biojs-vis-sequence: resourcify:  /build/sequence.js
brows debug biojs-vis-sequence: starting resourcify
brows debug biojs-vis-sequence: starting configy
main error Error: [TypeError: must start with number, buffer, array or string]
stderr:  npm WARN deprecated graceful-fs@3.0.8: graceful-fs version 3 and before will fail on newer node releases. Please update to graceful-fs@^4.0.0 as soon as possible.
npm WARN deprecated lodash@1.0.2: lodash@<3.0.0 is no longer maintained. Upgrade to lodash@^4.0.0.
npm WARN deprecated graceful-fs@1.2.3: graceful-fs version 3 and before will fail on newer node releases. Please update to graceful-fs@^4.0.0 as soon as possible.

main info msa: finished -> mako
brows debug msa: starting browserify
brows debug msa: browserify basedir:/tmp/tmp-71377s4wj1s0/node_modules/msa
brows debug msa: exposing:  lib/index.js
brows debug msa: starting resourcify
brows debug msa: resourcify:  dist/msa.js
brows debug msa: starting resourcify
brows debug msa: resourcify:  css/msa.css
brows debug msa: starting configy
main error Error: [TypeError: must start with number, buffer, array or string]
main error Error: [TypeError: must start with number, buffer, array or string]
main error Error: [TypeError: must start with number, buffer, array or string]

Any insight on how to solve the problem?

Thanks!
@wilzbach
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The msa viewer quite recently switched to webpack, so the biojs2galaxy which uses browserify doesn't work for it.
A better approach would be build tool independent - pinging @jessica-jordan. Do you have any time or student who could focus on this problem? This is closely related to the upcoming Jupyter gsoc...

On April 26, 2016 2:28:19 AM GMT+03:00, girlwithglasses notifications@github.com wrote:

npm 2.14.12
biojs2galaxy 0.0.7

I've installed biojs2galaxy globally, and am now trying to install the
MSA module, but getting the following errors:

$ biojs2galaxy -o config/plugins/visualizations/ msa
#tmpdir:  /tmp/tmp-71377s4wj1s0
[ 'galaxy-biojs', 'galaxy-vis' ]
biojs-vis-sequence: installing
drawrnajs: installing
exelixis-galaxy: installing
msa: installing
workmen info # pkgs 4
main info exelixis-galaxy: finished -> mako
brows debug exelixis-galaxy: starting browserify
brows debug exelixis-galaxy: browserify
basedir:/tmp/tmp-71377s4wj1s0/node_modules/exelixis-galaxy
brows debug exelixis-galaxy: exposing:  lib/index.js
brows debug exelixis-galaxy: starting resourcify
brows debug exelixis-galaxy: resourcify:  /build/exelixis.js
brows debug exelixis-galaxy: starting resourcify
brows debug exelixis-galaxy: starting configy
stderr:  npm WARN unmet dependency
/tmp/tmp-71377s4wj1s0/node_modules/msa/node_modules/biojs-io-fasta/node_modules/biojs-io-parser
requires xhr@'^2.0.1' but will load
npm WARN unmet dependency
/tmp/tmp-71377s4wj1s0/node_modules/msa/node_modules/xhr,
npm WARN unmet dependency which is version 1.17.1
npm WARN unmet dependency
/tmp/tmp-71377s4wj1s0/node_modules/msa/node_modules/biojs-io-gff/node_modules/biojs-io-parser
requires xhr@'^2.0.1' but will load
npm WARN unmet dependency
/tmp/tmp-71377s4wj1s0/node_modules/msa/node_modules/xhr,
npm WARN unmet dependency which is version 1.17.1

main info drawrnajs: finished -> mako
brows debug drawrnajs: starting browserify
brows debug drawrnajs: browserify
basedir:/tmp/tmp-71377s4wj1s0/node_modules/drawrnajs
brows debug drawrnajs: exposing:  src/drawrna.js
brows debug drawrnajs: starting resourcify
brows debug drawrnajs: resourcify:  /build/drawrnajs.js
brows debug drawrnajs: starting resourcify
brows debug drawrnajs: resourcify:  /style/bootstrap.css
brows debug drawrnajs: resourcify:  /style/spectrum.css
brows debug drawrnajs: resourcify:  /style/style.css
brows debug drawrnajs: starting configy
main info biojs-vis-sequence: finished -> mako
brows debug biojs-vis-sequence: starting browserify
brows debug biojs-vis-sequence: browserify
basedir:/tmp/tmp-71377s4wj1s0/node_modules/biojs-vis-sequence
brows debug biojs-vis-sequence: exposing:  lib/index.js
brows debug biojs-vis-sequence: browserify require biojs-io-fasta
brows debug biojs-vis-sequence: starting resourcify
brows debug biojs-vis-sequence: resourcify: 
http://code.jquery.com/jquery-1.11.0.min.js
brows debug biojs-vis-sequence: resourcify:  /build/sequence.js
brows debug biojs-vis-sequence: starting resourcify
brows debug biojs-vis-sequence: starting configy
main error Error: [TypeError: must start with number, buffer, array or
string]
stderr:  npm WARN deprecated graceful-fs@3.0.8: graceful-fs version 3
and before will fail on newer node releases. Please update to
graceful-fs@^4.0.0 as soon as possible.
npm WARN deprecated lodash@1.0.2: lodash@<3.0.0 is no longer
maintained. Upgrade to lodash@^4.0.0.
npm WARN deprecated graceful-fs@1.2.3: graceful-fs version 3 and before
will fail on newer node releases. Please update to graceful-fs@^4.0.0
as soon as possible.

main info msa: finished -> mako
brows debug msa: starting browserify
brows debug msa: browserify
basedir:/tmp/tmp-71377s4wj1s0/node_modules/msa
brows debug msa: exposing:  lib/index.js
brows debug msa: starting resourcify
brows debug msa: resourcify:  dist/msa.js
brows debug msa: starting resourcify
brows debug msa: resourcify:  css/msa.css
brows debug msa: starting configy
main error Error: [TypeError: must start with number, buffer, array or
string]
main error Error: [TypeError: must start with number, buffer, array or
string]
main error Error: [TypeError: must start with number, buffer, array or
string]

Any insight on how to solve the problem?

Thanks!

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#1

@ialarmedalien
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I don't have much time to dedicate to this project, unfortunately -- I saw the tutorial on installing msa and wanted to add that to my local Galaxy installation. How easy would it be to manually do what biojs2galaxy is doing? Do you have any wrappers for MSA that were generated from versions before MSA switched to webpack? Presumably I could hack / adapt one and install MSA myself.

@wilzbach
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Have a look at
https://github.com/wilzbach/msa/blob/master/test.html

https://github.com/biojs/biojs2galaxy/tree/master/template

You need to manually update the variables in the dependencies. I will have a look whether I can find an old version.

@wilzbach
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I will have a look whether I can find an old version.

There you go:
msa.zip

If you want to update to a newer version, you probably only have to touch the msa.mako and replace the files in static.

@ialarmedalien
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That works beautifully, thank you! Since MSA is served from a CDN, I've made life easier for myself by replacing the local URLs with those from the CDN.

@wilzbach wilzbach mentioned this issue Nov 29, 2016
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@ialarmedalien @wilzbach