Question: about the tool dependency in Galaxy
gravatar for cagalli
4.0 years ago by
cagalli30 wrote:


After I follow the instructions of Installing Tools into Galaxy from Tool Shed,

what I get in installed tool shed repositories is installation status:Installed,missing tool dependencies.

But I have followed to change my code in config/galaxy.ini into

# Path to the directory in which tool dependencies are placed.  This is used by
# the tool shed to install dependencies and can also be used by administrators
# to manually install or link to dependencies.  For details, see:
# If this option is not set to a valid path, installing tools with dependencies
# from the Tool Shed will fail.
tool_dependency_dir = dependency_dir


and I have one document named dependency_dir in galaxy file.

then after I typed

$ echo $PATH
$ type bowtie

what I get is -bash: type: bowtie: not found.


I hope someone can help me,thank you


ADD COMMENTlink modified 4.0 years ago by Jennifer Hillman Jackson25k • written 4.0 years ago by cagalli30
gravatar for Nate Coraor
4.0 years ago by
Nate Coraor3.2k
United States
Nate Coraor3.2k wrote:

Galaxy allows administrators to install tools with or without their dependencies. This option is on the last page of the installation process.

To install dependencies after the tools have been installed, you do the following in Galaxy:

  1. Admin -> Manage installed tool shed repositories -> the tool
  2. In the "Tool dependencies" section, click the name of an uninstalled dependency
  3. Select any missing dependencies (or "all") and click the "Install" button.
ADD COMMENTlink written 4.0 years ago by Nate Coraor3.2k

thanks for your answer,but what I get in Admin ->Installed tool shed repositories what I get is

In file included from bwtaln.c:11: In file included from ./bwtaln.h:5: ./bwt.h:95:14: warning: inline function 'bwt_2occ' is not defined [-Wundefined-inline] inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol); ^ bwtaln.c:63:4: note: used here bwt_2occ(rbwt, k - 1, l, c, &ok, &ol); ^ 1 warning generated. In file included from bwtgap.c:4: In file included from ./bwtgap.h:4: ./bwt.h:96:14: warning: inline function 'bwt_2occ4' is not defined [-Wundefined-inline] inline void bwt_2occ4(const bwt_t *bwt, bwtint_t ......

what I can do it just 

Select/unselect all tool dependencies

bwa version 0.5.9    to install or uninstall it,then both of them turn into error......

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by cagalli30

It looks like installation of the dependency was attempted but it failed to compile. If you click the "bwa" link on that page it should take you to a file browser, where you should be able to find an INSTALLATION.log file, which should provide the full error message.

ADD REPLYlink written 4.0 years ago by Nate Coraor3.2k
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