Comments (6)
Edit: soft links seem to work just fine for resolving this. I'm on a Mac, but should be the same for Linux.
Example: ln -s /Users/jpummil/anaconda3/bin/makeblastdb /usr/local/bin/makeblastdb
Also had to do the same for "blastn" and "tblastn"...
from bandage.
This stuff is tricky. I tried to make Bandage just call which makeblastdb
to see where it is, but I fear that Bandage doesn't have access to the same PATH
variable as your shell or something. That would be why you can see it with which
but Bandage can't.
I'll have to look into this more to come up with a good solution. In the mean time, a workaround may be to put your BLAST in a more standard location, like /usr/bin
or /usr/local/bin
. Let me know if that works.
from bandage.
@rrwick - I'm having the same issue and placing BLAST in /usr/bin or /usr/local/bin hasn't solved it for me. I've tried adding BLAST in the same folder as Bandage and changing the $PATH accordingly, but to no avail. Do you have any other suggestions?
from bandage.
Same issue. Used 'conda to install BLAST, thus it's in a somewhat unique location:
uaf134253:~ jpummil$ which makeblastdb
/Users/jpummil/anaconda3/bin/makeblastdb
Considering a symbolic link to see if that will suffice....
from bandage.
+1 for all replies above.
Also, relating to @jpummil 's reply, /usr/local/bin
seems to be the "path-to-be" on Mac as the System Integrity Protection of current Mac OS X (High Sierra in my case) seems to prohibit the creation of symlinks in /usr/bin
, even when using sudo
.
from bandage.
This stuff is tricky. I tried to make Bandage just call
which makeblastdb
to see where it is
Hello
instead of wich
that may respond diferently given os, and or version used.
you may want to use command -v makeblastdb
instead of which
furthermore command is posix
from bandage.
Related Issues (20)
- export bubble unitigs?
- Are you guys still working on this? HOT 1
- Install error 1 HOT 2
- Load CSV data - extension request HOT 2
- "save path sequence to fasta" command line option HOT 1
- mac shortcut key problem HOT 1
- Bandage AppImage/AppDir requires the shared libraries libGL.so.1, libfontconfig.so.1, and libfreetype.so.6 HOT 5
- tilting BLAST hits titles
- Overlaps counted twice in "Total length (no overlaps)" calculation? HOT 1
- Packaging and compiling Bandage
- fasta file from other assembly
- What is the shape representing?
- Bandage image HOT 1
- can bandage display a verkko assembly?
- help with compiling for bioconda HOT 3
- Add size scale to static png´s.
- Issue in opening mac terminal
- Can't open graph path files
- install error HOT 8
- Node Custom Properties
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 bandage.