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lpantano / mirdeep2_core

Main core scripts for novel mirna discovery from bam files
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Problem in installing mirdeep2_0_0_8 #1

Closed aj03 closed 7 years ago

aj03 commented 7 years ago

Hi, I am having problem while installing mirdeep2. Any Solution for this???

perl install.pl . . randfold already installed, nothing to do ... Compress::Zlib already installed, nothing to do ... Font::TTf already installed, nothing to do ... PDF::API2 already installed, nothing to do ...

RNAfold was/is not installed properly ()

When i am running tutorial_dir/run_tut.sh its working properly but when running mirdeep2.pl for my data its throwing error (RNAfold error)

report.log: computing randfold p-values select_for_randfold.pl mirdeep_runs/run_17_11_2016_t_14_17_29/tmp/signature.arf mirdeep_runs/run_17_11_2016_t_14_17_29/tmp/precursors.str > mirdeep_runs/run_17_11_2016_t_14_17_29/tmp/precursors_for_randfold.ids started: 14:19:59 Use of uninitialized value $lng in numeric le (<=) at /opt/mirdeep2_0_0_8/src/select_for_randfold.pl line 266, line 118. Use of uninitialized value in numeric le (<=) at /opt/mirdeep2_0_0_8/src/select_for_randfold.pl line 686, line 118. Use of uninitialized value in numeric le (<=) at /opt/mirdeep2_0_0_8/src/select_for_randfold.pl line 714, line 118. Use of uninitialized value in numeric le (<=) at /opt/mirdeep2_0_0_8/src/select_for_randfold.pl line 686, line 118. .. . .

error.log: RNAfold: invalid option -- n

I tried with Sample Installation too...by downloading all necessary packages required () a bowtie short read aligner (http://bowtie-bio.sourceforge.net/index.shtml) b Vienna package with RNAfold (http://www.tbi.univie.ac.at/~ivo/RNA/) c.i SQUID library (http://selab.janelia.org/software.html) goto Squid and download it c.ii randfold (http://bioinformatics.psb.ugent.be/software/details/Randfold) d Perl package PDF::API2 (http://search.cpan.org/search?query=PDF%3A%3AAPI2&mode=all)

lpantano commented 7 years ago

Hi,

sorry about the issue. Actually this repo is used to create a bioconda package and ready to use through bioconda. That error seems to be a problem with rnafold version.

Can you tell me what version you have? maybe it is a question to update the command used inside the code.

I am out of town so I will look at this on Monday.

Cheers

sent not from my computer

On Nov 18, 2016, at 06:46, aj03 notifications@github.com wrote:

Hi, I am having problem while installing mirdeep2. Any Solution for this???

perl install.pl . . randfold already installed, nothing to do ... Compress::Zlib already installed, nothing to do ... Font::TTf already installed, nothing to do ... PDF::API2 already installed, nothing to do ...

RNAfold was/is not installed properly ()

When i am running tutorial_dir/run_tut.sh its working properly but when running mirdeep2.pl for my data its throwing error (RNAfold error)

report.log: computing randfold p-values select_for_randfold.pl mirdeep_runs/run_17_11_2016_t_14_17_29/tmp/signature.arf mirdeep_runs/run_17_11_2016_t_14_17_29/tmp/precursors.str > mirdeep_runs/run_17_11_2016_t_14_17_29/tmp/precursors_for_randfold.ids started: 14:19:59 Use of uninitialized value $lng in numeric le (<=) at /opt/mirdeep2_0_0_8/src/select_for_randfold.pl line 266, line 118. Use of uninitialized value in numeric le (<=) at /opt/mirdeep2_0_0_8/src/select_for_randfold.pl line 686, line 118. Use of uninitialized value in numeric le (<=) at /opt/mirdeep2_0_0_8/src/select_for_randfold.pl line 714, line 118. Use of uninitialized value in numeric le (<=) at /opt/mirdeep2_0_0_8/src/select_for_randfold.pl line 686, line 118. .. . .

error.log: RNAfold: invalid option -- n

I tried with Sample Installation too...by downloading all necessary packages required () a bowtie short read aligner (http://bowtie-bio.sourceforge.net/index.shtml) b Vienna package with RNAfold (http://www.tbi.univie.ac.at/~ivo/RNA/) c.i SQUID library (http://selab.janelia.org/software.html) goto Squid and download it c.ii randfold (http://bioinformatics.psb.ugent.be/software/details/Randfold) d Perl package PDF::API2 (http://search.cpan.org/search?query=PDF%3A%3AAPI2&mode=all)

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aj03 commented 7 years ago

Hi, When i am locating RNAFold version its showing this:

$locate RNAfold /opt/ViennaRNA-2.3.0/src/bin/RNAfold /opt/mirdeep2_0_0_8/essentials/ViennaRNA-1.8.4/Progs/RNAfold /usr/local/bin/RNAfold

$RNAfold -V RNAfold 2.3.0

lpantano commented 7 years ago

Hi,

Did you find something else? I tried to reproduce but it is difficult since it seems depend on the data.

On Nov 21, 2016, at 1:57 AM, aj03 notifications@github.com wrote:

Hi, When i am locating RNAFold version its showing this:

$locate RNAfold /opt/ViennaRNA-2.3.0/src/bin/RNAfold /opt/mirdeep2_0_0_8/essentials/ViennaRNA-1.8.4/Progs/RNAfold /usr/local/bin/RNAfold

$RNAfold -V RNAfold 2.3.0

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aj03 commented 7 years ago

Hi, Thanks lpantano. I have resolved this error. The RNAFold version which I had in /usr/local/bin was /opt/ViennaRNA-2.3.0/src/bin/RNAfold but mirdeep2 install.pl requires /opt/mirdeep2_0_0_8/essentials/ViennaRNA-1.8.4/ version. As soon as I changed it,it started working.

perl install.pl ###############################################################################################

Last update: May 18, 2016

This is the miRDeep2 installer.

It is tested under a bash and zsh shell

It will try to download all necessary files and install them.

# ############################################################################################### gcc version: 4.8.4-2ubuntu1~14.04.3) already installed, nothing to do ... Checking environment variables ... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 82714 100 82714 0 0 36581 0 0:00:02 0:00:02 --:--:-- 36582 bowtie already installed, nothing to do ... RNAfold already installed, nothing to do ... randfold already installed, nothing to do ... Compress::Zlib already installed, nothing to do ... Font::TTf already installed, nothing to do ... PDF::API2 already installed, nothing to do ...

Installation successful

lpantano commented 7 years ago

perfect!

On Dec 8, 2016, at 11:42 PM, aj03 notifications@github.com wrote:

Hi, Thanks lpantano. I have resolved this error. The RNAFold version which I had in /usr/local/bin was /opt/ViennaRNA-2.3.0/src/bin/RNAfold but mirdeep2 install.pl requires /opt/mirdeep2_0_0_8/essentials/ViennaRNA-1.8.4/ version. As soon as I changed it,it started working.

perl install.pl ###############################################################################################

Last update: May 18, 2016

This is the miRDeep2 installer.

It is tested under a bash and zsh shell

It will try to download all necessary files and install them.

############################################################################################### gcc version: 4.8.4-2ubuntu1~14.04.3) already installed, nothing to do ... Checking environment variables ... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 82714 100 82714 0 0 36581 0 0:00:02 0:00:02 --:--:-- 36582 bowtie already installed, nothing to do ... RNAfold already installed, nothing to do ... randfold already installed, nothing to do ... Compress::Zlib already installed, nothing to do ... Font::TTf already installed, nothing to do ... PDF::API2 already installed, nothing to do ...

Installation successful

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shashj199 commented 7 years ago

Hey,

I am getting the same error. But when I try to install, Vienna 1.8.4 it throws an error

gcc  -g -O2   -o RNAfold RNAfold.o ../lib/libRNA.a -lm 
Undefined symbols for architecture x86_64:
  "_HairpinE", referenced from:
      _fill_arrays in libRNA.a(libRNA_a-fold.o)
      _backtrack in libRNA.a(libRNA_a-fold.o)
      _circfold in libRNA.a(libRNA_a-fold.o)
      _stack_energy in libRNA.a(libRNA_a-fold.o)
      _energy_of_circ_struct in libRNA.a(libRNA_a-fold.o)
      _loop_energy in libRNA.a(libRNA_a-fold.o)
  "_LoopEnergy", referenced from:
      _fill_arrays in libRNA.a(libRNA_a-fold.o)
      _backtrack in libRNA.a(libRNA_a-fold.o)
      _circfold in libRNA.a(libRNA_a-fold.o)
      _stack_energy in libRNA.a(libRNA_a-fold.o)
      _energy_of_circ_struct in libRNA.a(libRNA_a-fold.o)
      _loop_energy in libRNA.a(libRNA_a-fold.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [RNAfold] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Output of RNAfold -V

RNAfold 2.3.5

Can you help me in installing Vienna 1.8.4?

Thanks

lpantano commented 7 years ago

Hi,

sorry to hear you have issues. I use conda environment to install all tools, so not sure what is going on here.

Any chance you can move to a conda environment and use bioconda to install the vienna suit?

On Jul 1, 2017, at 5:00 AM, shashj199 notifications@github.com wrote:

Hey,

I am getting the same error. But when I try to install, Vienna 1.8.4 it throws an error

gcc -g -O2 -o RNAfold RNAfold.o ../lib/libRNA.a -lm Undefined symbols for architecture x86_64: "_HairpinE", referenced from: _fill_arrays in libRNA.a(libRNA_a-fold.o) _backtrack in libRNA.a(libRNA_a-fold.o) _circfold in libRNA.a(libRNA_a-fold.o) _stack_energy in libRNA.a(libRNA_a-fold.o) _energy_of_circ_struct in libRNA.a(libRNA_a-fold.o) _loop_energy in libRNA.a(libRNA_a-fold.o) "_LoopEnergy", referenced from: _fill_arrays in libRNA.a(libRNA_a-fold.o) _backtrack in libRNA.a(libRNA_a-fold.o) _circfold in libRNA.a(libRNA_a-fold.o) _stack_energy in libRNA.a(libRNA_a-fold.o) _energy_of_circ_struct in libRNA.a(libRNA_a-fold.o) _loop_energy in libRNA.a(libRNA_a-fold.o) ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[2]: [RNAfold] Error 1 make[1]: [all-recursive] Error 1 make: *** [all] Error 2 Output of RNAfold -V

RNAfold 2.3.5 Can you help me in installing Vienna 1.8.4?

Thanks

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