Question: GMAP error: invalid literal for int() with base 10
gravatar for chenzhuod
8 months ago by
chenzhuod30 wrote:


I run gmap in local galaxy, but tool error:

invalid literal for int() with base 10:'--split-output=gmap_out'

sometimes just " invalid literal for int() with base 10:'' "

How can I solve?


Siyuan Chen

gmap format galaxy local input • 441 views
ADD COMMENTlink modified 6 months ago by Nicola Soranzo70 • written 8 months ago by chenzhuod30
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:


There are two versions for GMAP/MiGMAP in the Tool Shed:

Both are a bit older and I am not sure of the exact usage or if there are any known issues. However, I can let you know that this error usually comes up when a tool is given an input that has formatting outside of what the 3rd party wrapped tool is expecting.

Example: MACS2 >> If unmapped reads are retained in a SAM input, there can be sequence identifiers that contain spaces, triggering this same error. For that case, there are two options: Remove the unmapped reads or convert the SAM (plain text) to BAM (binary) format to resolve the problem.

You'll need to review your inputs, this tool, and adjust to match what the tool is expecting. If you can't figure this out, do one of these (the second is much faster, as it is for most IUC tools):

  1. Both of the tool versions in the ToolShed have authors that can be reached for usage advice. How to: log in or create an account, navigate to the tool, and a method for contact is under "Repository Actions" in the top right corner ).

  2. Both authors can also be reached at the IUC Gitter channel for more direct communication plus help from the wider community who may be familiar with these older tool wrappers.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson25k

I decided to ask for help at Gitter to get this started. Please join in on the conversation and supply more details, or they might reply here and ask about that first unless this is a known (similar to the MACS2 issue):

ADD REPLYlink written 7 months ago by Jennifer Hillman Jackson25k

Thanks a lot ! and I add a custom GMAP to my local galaxy, eventually.

Another question about GMAP. I want to align genes to different reference sequences. but I'm not sure how many refererence sequences exactly. So, I hope to make a judge. It means if users have one reference, he just can align genes to the reference sequences one time. If he have two reference sequences, he can align them to the two sequences.

Can it come true by edit XML file?

I searched some answers. Someone said <if id="if-1"> <time from="5pm" to="9pm"/> </if> <then id="if-1"> <...some actions defined.../> </then> <else id="if-1"> <...other set of actions defined here.../> </else>

other said <xsl:choose>

<xsl:when test="expression">



<xsl:when test="expression">




    actions that occur if none of the above are detected



but they seems no effect.

Thanks, Siyuan

ADD REPLYlink written 7 months ago by chenzhuod30

Most if not all of the existing Galaxy tools allow the selection of a single target reference genome at runtime. If there are multiple genome targets, the tool could be put into a workflow multiple times and the jobs will run together.

That said, if you still want to explore this option, try using Planemo for development. If you need specific help with any part during/after the development process, please consider joining the development community: galaxy-dev Mailing list, galaxyproject/iuc Gitter, publishing tools to the ToolShed, etc.

ADD REPLYlink written 7 months ago by Jennifer Hillman Jackson25k
gravatar for Nicola Soranzo
6 months ago by
Norwich, UK
Nicola Soranzo70 wrote:

You should be able to fix the GMAP wrapper by applying this patch to the installed gmap.xml:

 diff -r 93911bac43da gmap.xml
--- a/gmap.xml  Thu Jan 05 14:31:24 2012 -0600
+++ b/gmap.xml  Wed May 09 23:42:32 2018 +0100
@@ -113,7 +113,7 @@
       #end if
     #end if
-    #if $split_output == True
+    #if $split_output
     #end if
     #if len($quality_protocol.__str__) > 0:
@@ -123,7 +123,7 @@
     #for $i in $inputs:
     #end for
-    #if $split_output == True
+    #if $split_output
       2> $gmap_stderr 
       2> $gmap_stderr > $output
ADD COMMENTlink written 6 months ago by Nicola Soranzo70
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