Unable to configure search engine

[mundoctor]

Describe the issue

I download RepeatMasker 4.1.5 and I want to configure it then I install RMblast 2.13.0 and hmmer 3.2.1 and trf 4.0.9 When I perl ./configure, and set the search engine, no matter I set RMblast or hmmer, it tell me "You must configure at least one search engine!" But I have set completely then. So it may be a bug of new version.

[rmhubley]

Thank you for the catch. This was a minor problem with the configure script. I have updated the 4.1.5 distribution to correct this issue. Please re-download 4.1.5 and let me know if you have any further issues.

[mundoctor]

Thank you for the catch. This was a minor problem with the configure script. I have updated the 4.1.5 distribution to correct this issue. Please re-download 4.1.5 and let me know if you have any further issues.

Thank you! rmhubley. Now I want to know if I can download the newest configure script only, or have to download all 4.1.5 distribution?

[Song-10-YF]

I download RepeatMasker 4.1.5, and after configuring it with rmblast-2.13.0 and hmmer-3.3.2, the similar error occured. "RepeatMasker version 4.1.0 Search engine ( ) is unknown to RepeatMasker. Please check the RepeatMaskerConfig.pm or rerun the configure script!." I would like to know if this is a bug in the new version or a problem with my configuration. Thanks and I look forward to your reply.

[rmhubley]

@mundoctor:

https://github.com/rmhubley/RepeatMasker/blob/master/configure

@Song-10-YF

Please try re-downloading the 4.1.5 distribution. If you downloaded prior to March 24th, the configure script had a small bug that caused this behavior.

[Song-10-YF]

Thank you! rmhubley. I also encountered some problems. For example, if LTR/DIRS and nLTR/DIRS appear in .out, and DIRS is counted with gypsy (Gypsy/DIRS1) in .tbl, will this situation lead to an increase in the number of pure Gypsy superfamilies? I would like to know the reason, thanks.

[bitahu]

i replaced the configure script with the configure txt from the above link (https://github.com/rmhubley/RepeatMasker/blob/master/configure) , and rerun perl ./configure , but still prompt Search engine ( ) is unknown to RepeatMasker. Please check the RepeatMaskerConfig.pm or rerun the configure script!.

[pckorhon]

Please don't update the distribution that is already publicly available - that creates only confusion. Instead, create a new distribution or a batch. Thank you!

[minhasbushra]

the problem still persists I downloaded it again today. should i get it form github instead of https://www.repeatmasker.org/RepeatMasker/ ?

[zhangwenda0518]

I also encountered this problem. I downloaded the latest version from github. still prompt Search engine ( ) is unknown to RepeatMasker. Please check the RepeatMaskerConfig.pm or rerun the configure script!. Any help？Thanks！

[rmhubley]

Finally figured out what was causing this for some people. Sorry for the long delay. To fix this before I can push out a new RepeatMasker release please edit your RepeatMaskerConfig.pm file and change the empty value field in the DEFAULT_SEARCH_ENGINE stanza:

          'DEFAULT_SEARCH_ENGINE' => {
                                       'command_line_override' => 'default_search_engine',
                                       'description' => 'The default search engine to use',
                                       'param_type' => 'value',
                                       'required' => 1,
                                       'value' => ''
                                     },

to the one of the following (based on the single engine you configured): 'rmblast', 'crossmatch', 'hmmer' or 'abblast'. For example, for rmblast it should look like:

          'DEFAULT_SEARCH_ENGINE' => {
                                       'command_line_override' => 'default_search_engine',
                                       'description' => 'The default search engine to use',
                                       'param_type' => 'value',
                                       'required' => 1,
                                       'value' => 'rmblast'
                                     },

In addition, you can remedy the problem without editing the file, if you supply the '-engine' option to RepeatMasker instead.

[sakusankun]

Finally figured out what was causing this for some people. Sorry for the long delay. To fix this before I can push out a new RepeatMasker release please edit your RepeatMaskerConfig.pm file and change the empty value field in the DEFAULT_SEARCH_ENGINE stanza:

          'DEFAULT_SEARCH_ENGINE' => {
                                       'command_line_override' => 'default_search_engine',
                                       'description' => 'The default search engine to use',
                                       'param_type' => 'value',
                                       'required' => 1,
                                       'value' => ''
                                     },

to the one of the following (based on the single engine you configured): 'rmblast', 'crossmatch', 'hmmer' or 'abblast'. For example, for rmblast it should look like:

          'DEFAULT_SEARCH_ENGINE' => {
                                       'command_line_override' => 'default_search_engine',
                                       'description' => 'The default search engine to use',
                                       'param_type' => 'value',
                                       'required' => 1,
                                       'value' => 'rmblast'
                                     },

In addition, you can remedy the problem without editing the file, if you supply the '-engine' option to RepeatMasker instead.

Thank you. That helps a lot!