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gkudla / hyb

hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data
GNU General Public License v3.0
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UNAfold #2

Closed brobr closed 6 years ago

brobr commented 8 years ago

Hi,

I just tried to install hyb on a mobile comp to be not so dependent on the university server and found: a) when running the INSTALL script, hyb cannot find the path to its own installation in /usr/local/hyb/bin (this can be corrected by exporting this to $PATH before running the script again) b) that a $200 academic license for UNAfold is needed to continue the installation (this is not in the software list of Biolinux 8). At the moment the script chokes on: /usr/local/hyb/bin/hyb:320: *** "hyb: UNAfold not installed". Stop. According to the hyb-script it seems that ViennaRNA could also be used. Would it be possible to alter the script so that it discovers which folding program is installed on a computer and can be used as the default? c) In relation to this, it would be helpful to list in a README file all the programs on which hyb depends for proper running and that have to be installed by the user beforehand (i.e. bowtie2, ViennaRNA/UNAfold, flexbar).

tony-travis commented 8 years ago

On 02/03/16 19:43, brobr wrote:

Hi,

I just tried to install hyb on a mobile comp to be not so dependent on the university server and found: a) when running the INSTALL script, hyb cannot find the path to its own installation in /usr/local/hyb/bin (this can be corrected by exporting this to $PATH before running the script again)

Hi, brobr.

Thanks for reporting the issue: I've changed the INSTALL script to add ${HYB_HOME}/bin to the PATH for the test-run and output a message to say you have to add ${HYB_HOME}/bin to your PATH after installation.

b) that a $200 academic license for UNAfold is needed to continue the installation (this is not in the software list of Biolinux 8). At the moment the script chokes on: |/usr/local/hyb/bin/hyb:320: *\ "hyb: UNAfold not installed". Stop.| According to the hyb-script it seems that ViennaRNA could also be used. Would it be possible to alter the script so that it discovers which folding program is installed on a computer and can be used as the default?

The error message is misleading: You don't need to install "UNAfold", you just need to install the "bio-linux-oligoarrayaux" package, which contains the "hybrid-min" program used by "hyb" for the default:

fold=UNAfold

We prefer to keep "UNAfold" as the default, so I'll change the error message to suggest installing the "bio-linux-oligoarrayaux" package.

c) In relation to this, it would be helpful to list in a README file all the programs on which hyb depends for proper running and that have to be installed by the user beforehand (i.e. bowtie2, ViennaRNA/UNAfold, flexbar).

Quite right - I've been asked to do that several times already!

HTH,

Tony.

Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis@minke-informatics.co.uk

brobr commented 8 years ago

Hi Tony, Thanks for the quick and adequate response. Installing the OligoArrayAux software from http://unafold.rna.albany.edu/?q=DINAMelt/OligoArrayAux worked (after adding it to the $PATH): the INSTALL script of Hyb ran to completion; the last line was: rm testdata_TEMP_FILE1_TXT testdata_TEMP_FILE1_TAB testdata_comp_hOH7_hybrids_ua.bit_1.fasta-comp_hOH7_hybrids_ua.bit_2.fasta.ct bash-4.3#

Cheers,

Rob