For the woefully inept, where in the heck is galaxy.ini stored?
I saw the documentation that said change 127.0.0.1 to 0.0.0.0 and the file name, can't find it to do so.
I know it all works as I've installed a module and that all shows up and works on localhost.
I have a galaxy installation on an OSX system that has been running fine
with our custom tools. However, now we want to start using for some simple
When I go to the main toolshed to install bwa, it lists the following
Repository *package_bwa_0_7_10_039ea20639* revision *5b9aca1e1c07* owned by
*devteam*Repository *package_samtools_1_1* revision *43f2fbec5d52* owned by
However, when running through this process, it fails at the
package_samtools_1_1 stage with an Error. Looking at the INSTALLATION.LOG i
see the following.
sed -i 's/-lcurses/-lncurses/' Makefile
sed -i 's/-lcurses/-lncurses/' Makefile
sed: 1: "Makefile": invalid command code M
However, looking at the tool_dependencies.xml for this particular package,
I see the following. I've highlighted in yellow a key configuration.
<package name="samtools" version="1.1">
<actions architecture="x86_64" os="linux">
<package name="ncurses" version="5.9">
name="package_ncurses_5_9" owner="iuc" prior_installation_required="True"
<package name="zlib" version="1.2.8">
name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True"
name="package_ncurses_5_9" owner="iuc" toolshed="
<package name="ncurses" version="5.9" />
name="package_zlib_1_2_8" owner="iuc" toolshed="
<package name="zlib" version="1.2.8" />
<action type="shell_command">sed -i
<action type="shell_command">sed -i -e
"s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2
So, to me, it sounds like this is trying to compile/install a distribution
meant for linux, but I'm on OSX. I was able to successfully install
samtools 1.2 with no errors.
Is there anyway to update, or modify the code for the BWA installation
recipe to use as a dependency samtools 1.2 rather then 1.1? Or does anyone
have any suggestions on how to get samtools 1.1 to work?
I tried making a bin/ directory and moving a precompiled samtools binary
for 1.1 in the directory. But galaxy didn't seem to recognize that the
dependency was satisfied manually.
Any advice would be greatly appreciated.
Thank you for the excellent training session on using ipython in galaxy.
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 .
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(a)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
npm ERR! weird error 127
npm ERR! not ok code 0
Galaxy master revision:6f53676f482634212bac512ec91dbf24e4afacff
(also tried against today's dev)
Distributor ID: Ubuntu
Description: Ubuntu 14.04.2 LTS
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
PS. Below is the content of: /usr/share/doc/nodejs/README.Debian
nodejs for Debian
The global search path for modules is
Future packages of node modules will use that directory,
so it should be used wisely.
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.
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"
Scripts calling Node.js as a shell command must be changed to instead
use the "nodejs" command.
my tool creates dynamically 96 datasets bundled into a list.
In the history I can see the number 96 in the top as hidden datasets
(6 shown, 96 hidden)
When I open the list, I just can see 64 items.
Now I run the job again and I have 96 more hidden items.
I open the new list and can see 66 items in that new list.
What is going on here?
Is that "just" a visual bug?
Or are my datasets affected?
PS: I use postgres
Dear Galaxy Community,
as we tried to establish the mail functionalities for our Galaxy instance, we managed to send email upon the "I forgot my password" user request. In the Email a Link is provided. Here two errors arise:
1. In the File "galaxy/lib/galaxy/webapps/galaxy/controllers/user.pyc" HTML Tags for this Email are generated, but the Email is send as plain/text, therefore the HTML Tags, as well as the (doubled) Link are visible for the user.
2. In our case, the provided link takes us to the normal user login page, where the user has no option of resetting his/her password.
Can you provide me some assistance to tackle the problems?
Makeblastdb can spit out warning notices when a higher count of N ambiguous nucleotides occurs in the first row of fasta data, but goes ahead and completes the blast database.
"Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is about 45% ambiguous nucleotides (shouldn't be over 40%)"
At moment the NCBI Blast+ wrappers (toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.01) are saying "yup those are errors", but i think they should be downgraded to just Notices? If the tool is part of a workflow it fails - on db's like RDP RNA this is quite a nuisance.
Anyone else run into the same thing?
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
I used Galaxy for several months when I had to use the reset password
I tried to reset my password, using the googlemail.com address that I used
in the original registration, several times but no "Galaxy Password Reset"
email are coming though. Out of the 4 or-so requests, only one reset email
came through hours later in the spam folder. The reset password that I got
The Galaxy website recommends to "contact an administrator" but this but I
can't find an email address or web form for that. Can you offer any help
with this issue?
Hello Galaxy Dev,
I have a question regarding parallelism on a BAM file.
I have currently implemented 3 split options for the BAM datatype
1) by_rname -> splits the bam into files based on the chromosome
2) by_interval -> splits the bam into files based on a defined bp length,
and does so across the entire genome present in the BAM file
3) by_read -> splits the bam into files based on the number of reads
encountered (if multiple files, all other files match the interval as the
Now, as you can imagine, reading and writing large BAM files is a pain, and
I personally think this is not the best solution for Galaxy.
What I was hoping to implement (but don't know how) is to create a new
metadata option in bam (bam.metadata.bam_interval) which would generate the
interval without creating a new file (essentially, I would create a symbolic
link to the old large file, and then update the metadata.bam_interval, this
would contain some string of the form chrom:start-end which could then be
used in a variety of tools which accept an interval as an option (for
example samtools view))
This would be far more efficient then my first implementation, but the thing
I don't know how to do is specify some kind of metadata at the split level.
I was hoping maybe you could direct me to an example that does this?
I have added the following to my metadata.py file:
class IntervalParameter( MetadataParamter )
def __init__( self, spec ):
MetadataParamter.__init__( self, spec ):
self.rname = self.spec.get( "rname" )
self.start = self.spec.get( "start" )
self.end = self.spec.get( "end" )
if self.rname = 'all':
return ''.join([self.rname, ':', self.start, '-', self.end])
And the following to my binary.py file:
### UNDER THE BAM CLASS
MetadataElement( name="bam_interval", desc="BAM Interval",
param=metadata.IntervalParameter, rname="all", start="", end="",
I somehow want rname="all" to be the default, but upon parallelism, I want
to be able to adjust this parameter in the split functions.
<parallelism method="multi" split_inputs="normal,tumour"
split_mode="by_interval" split_size="50000000" merge_outputs="output"/>
Would actually change the metadata of each file, and not create sub-bams.
For some of the recent tools we have developed on our Galaxy instance (
we were using the approach mentioned in the wiki for writing a single HTML
output file with links to additional output files (images, csv etc.,). This
is much nicer than generating multiple output files in the history panel.
However, the exported histories did not contain these included files. I
have now fixed this bug on our instance and have also created a pull
request on Github (#417 <https://github.com/galaxyproject/galaxy/pull/417>
1. Include the extra_files_path attribute on the dataset which is being
2. Check if there are any files in the extra_files_path for each dataset
that will be included in the archive.
3. If there are files present, create a new directory and save files to
this directory. This directory will then be included in exported archive.
The dataset's history ID is appended to both the directory and the
dataset's name to prevent conflict with a dataset of the same name.
A simple tool to test html export with included files is available at: