Body: <p>I am trying to predict transmembrane protein using <code>tmhmm-2.0c</code>. According to Package instruction, I have changed the path of perl inside the program like as following:</p>
  <p>First i checked the location of perl</p>
  <pre><code>which perl
  /usr/bin/perl
  </code></pre>
  <p>Then I checked the version also to make sure it is above 5.</p>
  <pre><code>perl -v 
  This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi (with 44 registered patches, see perl -V for more detail)
  
  Copyright 1987-2012, Larry Wall
  </code></pre>
  <p>I have pasted the path (<code>/usr/bin/perl</code>) in the <code>tmhmm</code> and <code>tmhmmformat.pl</code>
  Run the cmd:</p>
  <pre><code>./tmhmm --short &lt; /mnt/genome3/Lab_Users/Kishor/DISK_3/mnspt1/blood/rsem_outdir/blood.Trinity.RSEM.retained.clustered.fasta.transdecoder.pep &gt; tmhmm.out
  </code></pre>
  <p>But I only received a blank folder. It will be great for me if I get any suggestions to solve the problem.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-08T14:34:01.140Z
Comments.Text: You're right about the Perl path, both in the tmhmm and the tmhmmformat.pl file, but if you select the short option you will not get the output to create the output plot in the folder, that is why is empty.
Comments.UserDisplayName: zorbax
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-08T16:46:30.473Z
Comments.Text: Thanks Zora. But also tried without setting parameter '--short' and still didnt find output except a blank folder. I actually need following typr of output to fed into Trinotate:
  
  
  
  
  
  TRINITY_DN100_c0_g1_i1.p1 len=115 ExpAA=0.00 First60=0.00 PredHel=0 Topology=i
  
  TRINITY_DN102_c0_g2_i1.p1 len=256 ExpAA=0.16 First60=0.07 PredHel=0 Topology=o
  
  TRINITY_DN103_c0_g1_i1.p1 len=107 ExpAA=16.73 First60=0.00 PredHel=0 Topology=o
  
  
  Can you give me any other suggestion?
Comments.UserDisplayName: Kishor Kumar Sarker
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-08T17:07:41.973Z
Comments.Text: can you share minimal input to reproduce your error?
Comments.UserDisplayName: zorbax
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-11-24T17:35:59.337Z
Comments.Text: @zorbax
  Thanks for your concern. I have solved the issue. Needed to do some change inside the  tmhmm program.
Comments.UserDisplayName: Kishor Kumar Sarker
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-12-15T05:37:19.467Z
Comments.Text: Hi Kishor Kumar Sarker What changes you had done inside the tmhmm program?????? I also got the empty folder.
  Dimple
Comments.UserDisplayName: Dimple
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-12-16T11:17:35.577Z
Comments.Text: Hi @Dimple,
  In following link you will find the detail about the problem and as well as the solution at the end.
  https://github.com/Trinotate/Trinotate/issues/77
Comments.UserDisplayName: Kishor Kumar Sarker
Tags: <linux><software-installation><perl>
Title: tmhmm installation and running
ThreadText: # tmhmm installation and running
  
  (Asked by: username_0 on 2021-10-08)
  
  I am trying to predict transmembrane protein using `tmhmm-2.0c`. According to Package instruction, I have changed the path of perl inside the program like as following:
  
  First i checked the location of perl
  
  ```
  which perl
  /usr/bin/perl
  
  ```
  
  Then I checked the version also to make sure it is above 5.
  
  ```
  perl -v 
  This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi (with 44 registered patches, see perl -V for more detail)
  
  Copyright 1987-2012, Larry Wall
  
  ```
  
  I have pasted the path (`/usr/bin/perl`) in the `tmhmm` and `tmhmmformat.pl`
  Run the cmd:
  
  ```
  ./tmhmm --short < /mnt/genome3/Lab_Users/username_0/DISK_3/mnspt1/blood/rsem_outdir/blood.Trinity.RSEM.retained.clustered.fasta.transdecoder.pep > tmhmm.out
  
  ```
  
  But I only received a blank folder. It will be great for me if I get any suggestions to solve the problem.
  
  **Tags:** linux, software-installation, perl
  
  > **Comments:**
  > **username_1**: You're right about the Perl path, both in the tmhmm and the tmhmmformat.pl file, but if you select the short option you will not get the output to create the output plot in the folder, that is why is empty.  
  > **username_0**: Thanks Zora. But also tried without setting parameter '--short' and still didnt find output except a blank folder. I actually need following typr of output to fed into Trinotate:      TRINITY_DN100_c0_g1_i1.p1 len=115 ExpAA=0.00 First60=0.00 PredHel=0 Topology=i  TRINITY_DN102_c0_g2_i1.p1 len=256 ExpAA=0.16 First60=0.07 PredHel=0 Topology=o  TRINITY_DN103_c0_g1_i1.p1 len=107 ExpAA=16.73 First60=0.00 PredHel=0 Topology=o   Can you give me any other suggestion?  
  > **username_1**: can you share minimal input to reproduce your error?  
  > **username_0**: @username_1 Thanks for your concern. I have solved the issue. Needed to do some change inside the  tmhmm program.  
  > **username_2**: Hi username_0 Kumar username_0 What changes you had done inside the tmhmm program?????? I also got the empty folder. username_2  
  > **username_0**: Hi @username_2, In following link you will find the detail about the problem and as well as the solution at the end. https://github.com/Trinotate/Trinotate/issues/77  
  
  ---
  
  ## 0 answers
  
  