HmmUFOtu on conda? #7
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Hi, We use conda environments to manage all supported software, so having your tool in bioconda would accelerate its integration. |
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Hi Alessio,
Thanks for being interested in HmmUFOtu.
For question 1, no, since it is not a typical "Python dependency mess" tool
that need some specific environment to run and install. It is a
stand-alone, pure C++ tool that if can be ./configured, it will run. No
silly environment settings needed.
For question 2, yes. Follow the "homepage" link to HmmUFOtu home page, read
it carefully, and you will find your answer how.
If you have any questions, please let me know.
Best
Qi
…On Fri, May 8, 2020 at 7:11 AM Alessio Milanese ***@***.***> wrote:
HI Qi,
you did a nice tool!
I have two questions:
1. Are you planning to add HmmUFOtu to bioconda?
2. I would be interested to use your p7 HMM architecture. Something
similar to:
Given a MSA (<msafile>) and some sequences that I want to "align"
according to this existing MSA (<seqfile>):
hmmbuild hmm_file <msafile>
hmmalign hmm_file <seqfile>
Is that possible?
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Thanks for the fast response Qi, I cannot manage to install it on macOS:
I have Boost and Eigen3. I was wondering about bioconda because it would make it easier, and get you more visibility. On bioconda there are not only python packages (example HMMER). |
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Hi Qi. I think you are mistaken about what is Conda. Because compiling them on unix/mac or sometimes windows using a conda environement will garantee that all necessary dependancies are fulfilled (avoiding the issues encountered by Alessio above). Actually, I was considering to build myself a conda package for hmmUFOtu at some point, this is why I jumped into this conversation . The bioconda community is becoming huge and many tools are added there by the user community. Eventually, we could do this together (I already pushed some of my own sofware to bioconda and know the procedure). What do you think ? |
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Hi Benjamin,
I understand your point of Conda, it is just not my preference. HmmUFOtu
does depend on C++ boost (>1.50.0), Eigen3 headers for matrix operations,
and zlib for compressed files. It optionally depends on jsoncpp, but not
required. No other dependency as I know. If you run ./configure --help, you
will see all listed dependencies (--with-xxx section).
As for your error, looks like you don't have Eigen3. It is a C++ header
only library (no installation required). Please install Eigen3, and make
sure its root path (Eigen) is in your lib path. Thanks
Best regards
Qi
…On Fri, May 8, 2020 at 12:11 PM Benjamin Linard ***@***.***> wrote:
Hi Qi.
I think you are mitaken about what is Conda.
Conda do not mean only solving python issues, but any compilations issues.
It is a general environement manager, you can perfectly set different GCC
versions, different c libraries versions... in a conda environement. You
find find software such as raxml, hmmer ... on conda. Because compiling
them on unix/linux or sometimes windows using a conda environement will
garantee that all necessary dependancies are fulfilled (avoiding the issues
encountered by Alessio above).
Actually, I was considering to build myself a conda package for hmmUFOto
at some point, this is why I jumped into this conversation .
Eventually, we could do this together (I already pushed some of my own
sofware to bioconda).
What I need from you side is the complete list a C++ dependencies
necessary to build HmmOFUtu, including precise versions of those libraries.
What do you think ?
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Hi Qi, Thanks for the help.
It was installed already, I solved by: Or at least I think I solved it, because now I have a different error: Error
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Looking at stackoverflow I found that:
So I tried to download release v1.5.1. And now I'm back to the previous error: Maybe I misunderstood this:
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Hi,
First, $PATH is for executables, not for libraries. You should set CPPFLAGS
prior to run ./configure.
Second, the correct path should not include the "Eigen", which should be
/usr/local/Cellar/eigen/3.3.7/include/eigen3
Best
Qi
…On Fri, May 8, 2020 at 6:39 PM Alessio Milanese ***@***.***> wrote:
Looking at stackoverflow
<https://stackoverflow.com/questions/33278928/how-to-overcome-aclocal-1-15-is-missing-on-your-system-warning>
I found that:
This is usually caused by checking out code from Git instead of extracting
it from a .zip or .tar.gz archive. In order to trigger rebuilds when files
change, Git does not preserve files' timestamps, so the configure script
might appear to be out of date. As others have mentioned, there are ways to
get around this if you don't have a sufficiently recent version of
autoreconf.
So I tried to download release v1.5.1. And now I'm back to the previous
error:
mv -f .deps/ProgEnv.Tpo .deps/ProgEnv.Po
rm -f libEGUtil.a
ar cru libEGUtil.a CommandOptions.o ProgLog.o StringUtils.o TSVRecord.o TSVScanner.o VersionSequence.o ProgEnv.o
ranlib libEGUtil.a
Making all in math
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-am
g++ -DHAVE_CONFIG_H -I. -I/include -I/usr/local/include -g -O2 -MT Stats.o -MD -MP -MF .deps/Stats.Tpo -c -o Stats.o Stats.cpp
In file included from Stats.cpp:8:
./Stats.h:19:10: fatal error: 'Eigen/Dense' file not found
#include <Eigen/Dense>
^~~~~~~~~~~~~
1 error generated.
make[3]: *** [Stats.o] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1
Maybe I misunderstood this:
and make sure its root path (Eigen) is in your lib path.
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Following up on this conversation several years later, #11 shows HmmUFOtu does not compile using a version of Eigen3 which is too new. This is why a bioconda package, which would include a dependency on the exact version(s) of Eigen which are known to work with HmmUFOtu, would be useful. |
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Thanks for the good advice. I will try to get a bioconda version for it
when possible.
Best
Qi
…On Thu, Oct 3, 2024 at 1:47 PM brendanf ***@***.***> wrote:
Following up on this conversation several years later, #11
<#11> shows HmmUFOtu does not
compile using a version of Eigen3 which is too new. This is why a bioconda
package, which would include a dependency on the exact version(s) of Eigen
which are known to work with HmmUFOtu, would be useful.
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HI Qi,
you did a nice tool!
I have two questions:
Given a MSA (
<msafile>) and some sequences that I want to "align" according to this existing MSA (<seqfile>):Is that possible?
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