Comments (9)
thanks for the information.
can you run our tutorial:
http://www.regulatory-genomics.org/hint/tutorial/
and see if it works?
Maybe setting environment variable GS_LIB will fix it:
GS_LIB=/usr/share/ghostscript/8.70/lib:/usr/share/ghostscript/8.70/Resource/Init/
Meanwhile, I will try to reproduce the error.
from reg-gen.
Hi @mdurante1 ,
It seems that rgt-hint cannot find Ghostscript.
In rgt-hint differential, we use command 'epstopdf' to convert the plots from .eps to .pdf,
can you check if you can run this command successfully on you machine?
Thanks,
from reg-gen.
Yes, this command works
(atac_danpos) [mdurante@pegasus hint]$ epstopdf
EPSTOPDF 2.9.5gw, 2006/01/29 - Copyright 1998-2006 by Sebastian Rahtz et al.
Syntax: epstopdf [options] <eps file>
Options:
--help: print usage
--outfile=<file>: write result to <file>
--(no)filter: read standard input (default: false)
--(no)gs: run ghostscript (default: true)
--(no)compress: use compression (default: true)
--(no)hires: scan HiResBoundingBox (default: false)
--(no)exact: scan ExactBoundingBox (default: false)
--(no)debug: debug informations (default: false)
Examples for producing 'test.pdf':
* epstopdf test.eps
* produce postscript | epstopdf --filter >test.pdf
* produce postscript | epstopdf -f -d -o=test.pdf
Example: look for HiResBoundingBox and produce corrected PostScript:
* epstopdf -d --nogs -hires test.ps>testcorr.ps
!!! Error: Input filename missing!
from reg-gen.
Hi, @mdurante1
well, to make sure it works correctly, can you download the below example file and try to convert it to pdf using command:
epstopdf example.eps
https://www.dropbox.com/s/f6wul0ibbofiyiu/example.eps?dl
Thanks,
from reg-gen.
Yes, it's working correctly:
from reg-gen.
ok, thanks.
It would better if you can provide more information about your:
- opertion system (Ubuntu? Centos? or MacOS)
- python version
- rgt version
In addtion, please check if the file gs_init.ps exists on you machine using command:
locate gs_init.ps
I find some people also reported this problem:
https://bugs.launchpad.net/ubuntu/+source/ghostscript/+bug/262000
https://bbs.archlinux.org/viewtopic.php?id=1331
from reg-gen.
(atac_danpos) [mdurante@pegasus ~]$ rgt-motifanalysis --version
Motif Analysis - Regulatory Analysis Toolbox (RGT) - v0.11.1
(atac_danpos) [mdurante@pegasus ~]$ python --version
Python 2.7.14
(atac_danpos) [mdurante@pegasus ~]$ cat /etc/centos-release
CentOS release 6.5 (Final)
(atac_danpos) [mdurante@pegasus ~]$ locate gs_init.ps
/usr/share/ghostscript/8.70/Resource/Init/gs_init.ps
I am also seeing this same issue separately on Ubuntu 16.04 with the same version of python and rgt
from reg-gen.
I can't reproduce the error on Ubtuntu 16.04 and CentOS Linux release 7.3.1611, so far.
Hi, @mdurante1
Can you download the below file and run test script on you machine.
test.tar.gz
it will create a .pdf and .eps file by merging the line plot and weblogo file, if everything is working.
Thanks,
from reg-gen.
Hi @lzj1769
I was able to fix this error by setting the environment variable GS_LIB.
Thanks for all of your help.
Best,
Michael
from reg-gen.
Related Issues (20)
- invalid load key, '\x00'
- RGT installation successful, but rgtdata folder is missing. HOT 5
- Question regarding how Lineplots values are calculated, related to #116 HOT 1
- Issue running on Macbook Pro M1 HOT 18
- Motif enrichment scores HOT 1
- #The version of JASPAR HOT 1
- Number of success in mpbs.bed and fulltest_statistics.txt files did not match
- ResourceWarning: unclosed file (Enable tracemalloc to get the object allocation traceback)
- RGT Hint differential error HOT 5
- Transcription factor scatter plot HOT 2
- aarch64 support
- Result file description
- Fold-change values in THOR differential peaks and post-processed bigwigs
- Extension sizes estimated with THOR HOT 1
- Error in rgt-hint differential for my own data
- Deprecation warnings, non-compatibility with python 3.12, libpng12.so.0
- failed installation on Mac mini with Apple M2 Chip HOT 1
- rgt-THOR multiple warnings for wigToBigWig
- warnings/errors in rgt-THOR
- IndexError: index is out of bounds
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from reg-gen.