A question about install egg file on ubuntu10.10
 

Hi,Everyone,

I have got two egg format files <birdsuite-1.0-py2.5.egg and mpgutils-0.7-py2.5.egg> ,and intended to install on my ubuntu 10.10 platform.

Following the instructions googled on the web,the steps as follows:
1>sudo apt-get install python-setuptools
then cd to the directory contains the two egg files
2>sudo easy_install birdsuite-1.0-py2.5.egg
whereas the output came out to be :

bhli@ubuntu:~/EXEDIR$ sudo easy_install birdsuite-1.0-py2.5.egg
install_dir /usr/local/lib/python2.6/dist-packages/
Processing birdsuite-1.0-py2.5.egg
creating /usr/local/lib/python2.6/dist-packages/birdsuite-1.0-py2.5.egg
Extracting birdsuite-1.0-py2.5.egg to /usr/local/lib/python2.6/dist-packages
Adding birdsuite 1.0 to easy-install.pth file
Installing cn_locus_summarize script to /usr/local/bin
Installing cn_create_exclude_list script to /usr/local/bin
Installing cn_probeset_summarize script to /usr/local/bin
Installing birdsuite_report script to /usr/local/bin
Installing birdseedqc script to /usr/local/bin
Installing cn_annotate_allele_summary script to /usr/local/bin
Installing initializeCNGaussians script to /usr/local/bin
Installing post_birdseye script to /usr/local/bin
Installing pre_birdseye script to /usr/local/bin
Installing birdsuite_qc script to /usr/local/bin
Installing cn_create_illumnia_exclude_list script to /usr/local/bin

Installed /usr/local/lib/python2.6/dist-packages/birdsuite-1.0-py2.5.egg
Processing dependencies for birdsuite==1.0
Searching for birdsuite==1.0
Reading http://pypi.python.org/simple/birdsuite/
No local packages or download links found for birdsuite==1.0
error: Could not find suitable distribution for Requirement.parse('birdsuite==1.0')

1>what is the matter ?and where i am wrong ?
2>whether or not the egg files that are in zip format can be installed ?
3>what prerequisites should be required while installing egg file ?
4>Another one more question:
when installing a software ,the instructions require install python packages ,and I install the python on ubuntu10.10 by command:
sudo apt-get install python
How can I know the python path is correctly set or not? and Python and the pythoninstaller are the same software or not ?

Have you read the documentation and installation instructions from this site? Looks pretty detailed to me and what you posted seems to have left out a few steps?

http://www.broadinstitute.org/scienc...dsuite-install

I am a newbie on ubuntu.

Actually,I have read the documentation many times,whereas the software still cannot run correctly although I have installed the software following the instructions step by step.
Have you ever used this software ?and could you please help me installing Birdsuite ?
I have spent 3 weeks to learn installing this software,but till now it still cannot run correctly?

I have a request,I will write down all the details about the procedures I installed the software,and could you please give me some suggestions or advice after you reading it?
much obliged.

After installing a 64-bit ubuntu10.10 on a window XP hard disk.
1>I installed the JAVA by the following steps:

a)sudo add-apt-repository "deb http://archive.canonical.com/ubuntu maverick partner"
b)sudo apt-get update
c)sudo apt-get install sun-java6-jre sun-java6-jdk sun-java6-plugin
d)java -version
e)sudo update-alternatives --config java

2>then install the python 2.6 and numpy python package

sudo apt-get install python
sudo apt-get install numpy-python
sudo apt-get install scipy-python

3>install R and mclust R package

sudo apt-get install r-base
sudo R CMD INSTALL mclust_3.4.8.tar.gz

4>then begin the installation
a)Create a directory called EXEDIR on /home/bhli,and Unpack birdsuite_executables_1.5.5.tgz into EXEDIR.
b)copy the 64-bit version of apt-probeset-summarize into EXEDIR, with the name apt-probeset-summarize.64
c)Run the following commands:
R CMD INSTALL -l EXEDIR EXEDIR/broadgap.utils_1.0.tar.gz
(Before running this command,a little change have made to the broadgap.utils_1.0.tar.gz)
R CMD INSTALL -l EXEDIR EXEDIR/broadgap.cnputils_1.0.tar.gz
R CMD INSTALL -l EXEDIR EXEDIR/broadgap.canary_1.0.tar.gz
d)Install Matlab compiled runtime(and this step is ok)
e)Create a directory called METADATADIR on /home/bhli,and Unpack birdsuite_metadata_executables_1.5.5.tgz into METADATADIR.
f)Copy the following files from the Affymetrix library bundle (genomewidesnp6_libraryfile.zip) into METADATADIR: GenomeWideSNP_6.Full.cdf, GenomeWideSNP_6.specialSNPs.
g)Copy GenomeWideSNP_6.cdf into METADATADIR.
Copy apt-geno-qc (from APT) into EXEDIR.
h)Create a directory (TESTDIR) and unpack birdsuite_inputs_1.0.tgz there.
cd to TESTDIR.
Run the following command:

bhli@ubuntu:~/TESTDIR$ ~/EXEDIR/birdsuite.sh --basename=test --exeDir=/home/bhli/EXEDIR/ --metadataDir=/home/bhli/METADATADIR/ --chipType=GenomeWideSNP_6 --genderFile=test.gender --celFiles=test.cels --noLsf --apt_probeset_summarize.force --outputDir=output

+ unset DISPLAY
+ export MCR_INHIBIT_CTF_LOCK=1
+ MCR_INHIBIT_CTF_LOCK=1
++ /home/bhli/EXEDIR/getAbsPath /home/bhli/EXEDIR
+ exedir=/home/bhli/EXEDIR
+ export R_LIBS=/home/bhli/EXEDIR:
+ R_LIBS=/home/bhli/EXEDIR:
+ '[' -n 1 ']'
+ exedir_args=--exeDir=/home/bhli/EXEDIR
+ java -jar /home/bhli/EXEDIR/Birdsuite.jar --exeDir=/home/bhli/EXEDIR --basename=test --exeDir=/home/bhli/EXEDIR/ --metadataDir=/home/bhli/METADATADIR/ --chipType=GenomeWideSNP_6 --genderFile=test.gender --celFiles=test.cels --noLsf --apt_probeset_summarize.force --outputDir=output
Newer version of birdsuite available. Version running is 1.5.5 latest version is 1.5.2
Fri May 20 14:44:10 CST 2011 Calling /home/bhli/EXEDIR/apt-probeset-summarize.sh -a quant-norm.target=1000,pm-only,plier.optmethod=1,expr.genotype=true -o output --cdf-file /home/bhli/METADATADIR/GenomeWideSNP_6.Full.cdf --probeset-ids /home/bhli/METADATADIR/GenomeWideSNP_6.birdsuite_probelist --mem-usage 4000 --block-size 0 --precision 2 --force cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A01_31218.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A02_31234.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A03_31250.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A04_31266.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A05_31282.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A06_31298.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A07_31314.CEL cel/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A08_31330.CEL
Opening cdf file: GenomeWideSNP_6.Full.cdf
Expecting 1 iteration.
Doing iteration: 1
Opening cdf file: GenomeWideSNP_6.Full.cdf
Loading 1842537 probesets and 6675129 probes.
Reading 8 cel filesDone.
Processing Probesets......................Done.
Flushing output reporters. Finalizing output.
Done.
Cleaning up.
Done.
Run took approximately: 3.33 minutes.
Fri May 20 14:47:30 CST 2011 Done /home/bhli/EXEDIR/apt-probeset-summarize.sh
Fri May 20 14:47:30 CST 2011 Calling /home/bhli/EXEDIR/cn_annotate_allele_summary --probe_locus /home/bhli/METADATADIR/GenomeWideSNP_6.hg18.probe_locus -o output/test.annotated_summary -t output --summary output/test.allele_summary
Exception in thread "main" edu.mit.broad.mpgcore.exception.MPGRuntimeException: java.lang.reflect.InvocationTargetException
at edu.mit.broad.espcore.apps.affy.BirdSuite.run(BirdSuite.java:401)
at edu.mit.broad.espcore.apps.affy.BirdSuite.main(BirdSuite.java:296)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at edu.mit.broad.espcore.apps.affy.BirdSuite.run(BirdSuite.java:396)
... 1 more
Caused by: edu.mit.broad.mpgcore.exception.MPGRuntimeException: java.io.IOException: Cannot run program "/home/bhli/EXEDIR/cn_annotate_allele_summary": java.io.IOException: error=2, No such file or directory
at edu.mit.broad.espcore.apps.affy.BirdSuite.execWithStdOutputs(BirdSuite.java:359)
at edu.mit.broad.espcore.apps.affy.BirdSuite.annotate_allele_summaries(BirdSuite.java:478)
... 6 more
Caused by: java.io.IOException: Cannot run program "/home/bhli/EXEDIR/cn_annotate_allele_summary": java.io.IOException: error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
at java.lang.Runtime.exec(Runtime.java:593)
at edu.mit.broad.espcore.apps.affy.BirdSuite.execWithStdOutputs(BirdSuite.java:335)
... 7 more
Caused by: java.io.IOException: java.io.IOException: error=2, No such file or directory
at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
at java.lang.ProcessImpl.start(ProcessImpl.java:65)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
... 9 more


So what might be the problem and what should I do to resolve it?

Don't know. Never used it an don't plan to. The only thing problematic I see is:

Might check to see if that file exists. Looks like an interesting program. Hopefully someone with a little more knowledge about it will see your post. Good Luck.

Hi, yimaizhe!

I know the thread is old, but have you solved your problem? I am having a similar problem!

It may be a java problem, I guess, how did you got through this?
Thank you

you really should not be trying to run software from your "Desktop" folder
that is a special decorative folder

and some DM's will not let you
on others there might be problems

also Ubuntu 10 is a old, VERY OLD, and UNSUPPORTED operating system
please stay current and do a new install using Ubuntu 14.04 or 14.10

It is still possible to make use of
 

I agree this is a quite old thread: However, for those that find this through a web search and still have an interest to run birdsuite-1.5.5 .. got it working (this is a bit finicky now on newer Linux OS releases but still can be run).

The problem listed appears when using a version of Python (such as 2.6 or 2.7) which is newer and incompatible with the install.py (EasyInstall). Newer setuptools do not work with the birdsuite-1.0-py2.5.egg file, which provides the cn_allele_summary script among others during install (it is birdsuite FAQ#3 - Link[0]). As noted: this is a required script to have in the EXEDIR path for the pipeline being run.

The way this works is to make use of python-2.5.6 source and build it with the following modules: zlib, md5, sha, _sha256, _sda512 (of which zlib and sha256 are required to use an old release of setuptools). Setuptools may need to be installed from (either: bitbucket [4] or git) as opposed to pip - as newer setuptools in pip will not install correctly.

Links:
- [0]: https://www.broadinstitute.org/birdsuite/birdsuite-faq
- [1]: http://broad.mit.edu/ftp/pub/mpg/bir...Install_Py.pdf
- [2]: https://cstan.io/?p=11573&lang=en
- [3]: http://peak.telecommunity.com/DevCenter/EasyInstall
- [4]: https://pypi.org/project/setuptools/...on-2-5-support
- [5]: https://github.com/pypa/setuptools

There are additional steps required to make sure a newer OS such as Ubuntu 18 can make use of this software. For example..

1. I had to update the installed python scripts to include the correct PYTHONPATH, which for some reason doesn't get passed from java birdsuite.jar to the child process in the env, even though it was exported to the invoking process.

2. The MCR75Installer (https://www.linuxquestions.org/quest...-error-838281/ ) may need to have both the 64-bit and 32-bit installer extracted (-is:extract option) -- simply in order to run the provided setup.jar file.

In my case: The provided sun jre 1.5.0 in the 64-bit MCR installer didn't work (if it did before) on recent Ubuntu, but you can use the 32-bit sun JRE in one tempdir to run the 64-bit setup.jar in the other extracted tempdir, to provide the necessary libraries into your $EXEDIR/MCR75_glnxa64 birdsuite install path.