Hey, Seth

I'm using npm less 1.3.3. That error isn't a known issue, no.

Is that the full stack trace/error report? Which files have you edited?

Thanks, Carl

On Tue, Jul 30, 2013 at 2:39 PM, Seth Sims seth.sims@gmail.com wrote:

Dear Galaxy devs,

I am attempting to create a style directory to match my school's look

and feel. I am mainly trying to get the development environment setup to do this right now. My current problem is that when I attempt to compile the standard blue_colors.ini which comes with galaxy I am receiving a syntax error:

ParseError: Syntax Error on line 1 in /srv/galaxy-dist/static/style/blue_colors.ini:1:10 1 base_text=#303030 2 base_bg_top=#FFFFFF

I have not edited that file at all. So the first question is, what version of lessc is being used to compile the styles for the basic installation? Also are there any pitfalls I should be aware of with this process.

• Seth

---

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Here are a couple of questions on rsync: 1. the amount of files for hg19 and mm9 is extremely different (over 600 vs. 88 Gb) - why is that so? They are both mammalian genomes ... are there redundant files in hg19, is mm9 incomplete...? 2. if I list the directories for hg19 and mm9, there seems to be a group of files for bowtie2 in hg19, but not in mm9 - where are the ones for mm9? 3. genome sequences such as mm9.fa are not in /indexes, there are only pointers (mm9/bowtie_index/mm9.fa -> ../seq/mm9.fa ) can the sequence files be 'rsync'ed from somewhere?

Gerald

Dear Carl,

OK, I have been casting about to find out what the problem was; invoking lessc on the ini was just something I tried since the error from the makefile is completely opaque. I already had PIL and pyparsing installed, just checked again to make sure...

After fighting a bit with npm to get lessc installed I now have lessc-1.4.2 which is giving this error:

/srv/galaxy-dist/static/style$ sudo make OUT=blue make[1]: Entering directory `/srv/galaxy-dist/static/style/blue' lessc -x ../base.less base.css util.error: Use console.error instead ParseError: Unrecognised input in /srv/galaxy-dist/static/style/bootstrap/mixins.less on line 561, column 7: 560 .spanX (@index) when (@index > 0) { 561 (~".span@{index}") { .span(@index); } 562 .spanX(@index - 1);

make[1]: *** [base.css] Error 1 make[1]: Leaving directory `/srv/galaxy-dist/static/style/blue' make: *** [all] Error 2

So now I guess i'm going to try and downgrade specifically to lessc 1.3.3

- Seth

On Mon, Aug 5, 2013 at 11:56 AM, Carl Eberhard carlfeberhard@gmail.comwrote:

The ini file is not a .less file so it will error if you call lessc directly with it.

It may be that you're lacking some (not obvious) dependencies. Do you have pyparsing and PIL installed and available in your terminal (pip install will work with both)?

You can also use npm to update/install your node modules (sudo npm install -g less) if you have npm installed.

On Mon, Aug 5, 2013 at 11:28 AM, Seth Sims seth.sims@gmail.com wrote:

...

Dear Carl,

You are using a more recent version of lessc then I am so it is

probably just a versioning error. Ubuntu Precise Pangolin's repositories are still at lessc-1.2.1. So apparently I need to manually install a more recent version of the compiler. Here is a description of the error if anyone else has this problem:

I have not edited anything, when attempting to compile the vanilla

blue_colors.ini from the repo I receive an error like so:

$sudo lessc blue_colors.ini ParseError: Syntax Error on line 1 in /srv/galaxy-dist/static/style/blue_colors.ini:1:9 1 base_text=#303030 2 base_bg_top=#FFFFFF

However the only reason I used that command is because the makefile gives a different error:

$ sudo make OUT=blue make[1]: Entering directory `/srv/galaxy-dist/static/style/blue' lessc -x ../base.less base.css TypeError: Cannot call method 'charAt' of undefined at getLocation (/usr/lib/nodejs/less/parser.js:204:34) at new LessError (/usr/lib/nodejs/less/parser.js:213:19) at Object.toCSS (/usr/lib/nodejs/less/parser.js:379:31) at /usr/bin/lessc:103:28 at /usr/lib/nodejs/less/parser.js:428:40 at /usr/lib/nodejs/less/parser.js:94:48 at /usr/lib/nodejs/less/index.js:113:15 at /usr/lib/nodejs/less/parser.js:428:40 at /usr/lib/nodejs/less/parser.js:94:48 at /usr/lib/nodejs/less/index.js:113:15 make[1]: *** [base.css] Error 2 make[1]: Leaving directory `/srv/galaxy-dist/static/style/blue' make: *** [all] Error 2

Which is apparently a bug in the version of lessc I have.

On Mon, Aug 5, 2013 at 11:09 AM, Carl Eberhard carlfeberhard@gmail.comwrote:

...

Hey, Seth

I'm using npm less 1.3.3. That error isn't a known issue, no.

Is that the full stack trace/error report? Which files have you edited?

Thanks, Carl

On Tue, Jul 30, 2013 at 2:39 PM, Seth Sims seth.sims@gmail.com wrote:

...

Dear Galaxy devs,

I am attempting to create a style directory to match my school's

look and feel. I am mainly trying to get the development environment setup to do this right now. My current problem is that when I attempt to compile the standard blue_colors.ini which comes with galaxy I am receiving a syntax error:

ParseError: Syntax Error on line 1 in /srv/galaxy-dist/static/style/blue_colors.ini:1:10 1 base_text=#303030 2 base_bg_top=#FFFFFF

I have not edited that file at all. So the first question is, what version of lessc is being used to compile the styles for the basic installation? Also are there any pitfalls I should be aware of with this process.

• Seth

---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Nice catch. Maybe an old version of bootstrap's less. I'll see what I can do about that.

Thanks for the help.

On Mon, Aug 5, 2013 at 12:17 PM, Seth Sims seth.sims@gmail.com wrote:

Dear Carl,

lessc 1.3.3 successfully compiles the scripts. So you've got a bit of a goldielocks situation going on. Looks like only 1.3.* versions of less are useable with galaxy as it stands.

• Seth

On Mon, Aug 5, 2013 at 12:09 PM, Seth Sims seth.sims@gmail.com wrote:

...

Dear Carl,

OK, I have been casting about to find out what the problem was; invoking lessc on the ini was just something I tried since the error from the makefile is completely opaque. I already had PIL and pyparsing installed, just checked again to make sure...

After fighting a bit with npm to get lessc installed I now have

lessc-1.4.2 which is giving this error:

/srv/galaxy-dist/static/style$ sudo make OUT=blue make[1]: Entering directory `/srv/galaxy-dist/static/style/blue' lessc -x ../base.less base.css util.error: Use console.error instead ParseError: Unrecognised input in /srv/galaxy-dist/static/style/bootstrap/mixins.less on line 561, column 7: 560 .spanX (@index) when (@index > 0) { 561 (~".span@{index}") { .span(@index); } 562 .spanX(@index - 1);

make[1]: *** [base.css] Error 1 make[1]: Leaving directory `/srv/galaxy-dist/static/style/blue' make: *** [all] Error 2

So now I guess i'm going to try and downgrade specifically to lessc 1.3.3

• Seth

On Mon, Aug 5, 2013 at 11:56 AM, Carl Eberhard carlfeberhard@gmail.comwrote:

...

The ini file is not a .less file so it will error if you call lessc directly with it.

It may be that you're lacking some (not obvious) dependencies. Do you have pyparsing and PIL installed and available in your terminal (pip install will work with both)?

You can also use npm to update/install your node modules (sudo npm install -g less) if you have npm installed.

On Mon, Aug 5, 2013 at 11:28 AM, Seth Sims seth.sims@gmail.com wrote:

...

Dear Carl,

You are using a more recent version of lessc then I am so it is

probably just a versioning error. Ubuntu Precise Pangolin's repositories are still at lessc-1.2.1. So apparently I need to manually install a more recent version of the compiler. Here is a description of the error if anyone else has this problem:

I have not edited anything, when attempting to compile the vanilla

blue_colors.ini from the repo I receive an error like so:

$sudo lessc blue_colors.ini ParseError: Syntax Error on line 1 in /srv/galaxy-dist/static/style/blue_colors.ini:1:9 1 base_text=#303030 2 base_bg_top=#FFFFFF

However the only reason I used that command is because the makefile gives a different error:

$ sudo make OUT=blue make[1]: Entering directory `/srv/galaxy-dist/static/style/blue' lessc -x ../base.less base.css TypeError: Cannot call method 'charAt' of undefined at getLocation (/usr/lib/nodejs/less/parser.js:204:34) at new LessError (/usr/lib/nodejs/less/parser.js:213:19) at Object.toCSS (/usr/lib/nodejs/less/parser.js:379:31) at /usr/bin/lessc:103:28 at /usr/lib/nodejs/less/parser.js:428:40 at /usr/lib/nodejs/less/parser.js:94:48 at /usr/lib/nodejs/less/index.js:113:15 at /usr/lib/nodejs/less/parser.js:428:40 at /usr/lib/nodejs/less/parser.js:94:48 at /usr/lib/nodejs/less/index.js:113:15 make[1]: *** [base.css] Error 2 make[1]: Leaving directory `/srv/galaxy-dist/static/style/blue' make: *** [all] Error 2

Which is apparently a bug in the version of lessc I have.

On Mon, Aug 5, 2013 at 11:09 AM, Carl Eberhard <carlfeberhard@gmail.com

...

wrote:

...

Hey, Seth

I'm using npm less 1.3.3. That error isn't a known issue, no.

Is that the full stack trace/error report? Which files have you edited?

Thanks, Carl

On Tue, Jul 30, 2013 at 2:39 PM, Seth Sims seth.sims@gmail.comwrote:

...

Dear Galaxy devs,

I am attempting to create a style directory to match my school's

look and feel. I am mainly trying to get the development environment setup to do this right now. My current problem is that when I attempt to compile the standard blue_colors.ini which comes with galaxy I am receiving a syntax error:

ParseError: Syntax Error on line 1 in /srv/galaxy-dist/static/style/blue_colors.ini:1:10 1 base_text=#303030 2 base_bg_top=#FFFFFF

I have not edited that file at all. So the first question is, what version of lessc is being used to compile the styles for the basic installation? Also are there any pitfalls I should be aware of with this process.

• Seth

---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/