Answers.Body: <p>The short answer is to <a href="https://docs.conda.io/en/latest/miniconda.html" rel="nofollow noreferrer">use conda</a>. In the <a href="https://bioconda.github.io/" rel="nofollow noreferrer">bioconda channel</a> we have most of the tools used in bioinformatics, such as samtools. You do not need administrator permissions to install conda or packages with it, so your lack of <code>sudo</code> ability is not an issue.</p>
  
  <blockquote>
    <p>I have installed samtools and many other programs necessary for the workflow, however, once I am on the remote server in bash, and try and run a function over the files of interest, it gives me the error</p>
  </blockquote>
  
  <p>Installing packages on your local machine won't affect the remote server unless they share a file system, so this is expected.</p>
  
  <p>As an aside, BAM files aren't really "raw", they're considered processed data (fastq/fast5 files are considered truly "raw" data in the sequencing world).</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-02-12T20:40:14.337Z
Answers.LastActivityDate: 2019-02-12T20:40:14.337Z
Answers.UserDisplayName: Devon Ryan
Answers.Body: <p>At a very wild guess</p>
  
  <pre><code>-bash-samtools
  </code></pre>
  
  <p>This looks shaky. For a start you need a space between the command and the application in all Linux/Unix/Mac OS X applications (its complicated to explain right now [see below] just accept it).</p>
  
  <hr>
  
  <p>Wait you are using <code>sudo</code> and thats how you are installing on a local machine. <code>sudo</code> on a remote machine will never work, because you are not the systems admin. <code>sudo</code> on a local machine is not cool (see below)</p>
  
  <hr>
  
  <p>Anyway I need to do some next-gen and have 6 MiSeq kits waiting for action so I installed it from here:
  <a href="http://www.htslib.org/download/" rel="nofollow noreferrer">http://www.htslib.org/download/</a></p>
  
  <p>Okay so here's my tcsh history</p>
  
  <pre><code> 4  21:44   cd sam* # like I was in the Desktop
   7  21:44   more README # I needed to know how they wanted the installation
   8  21:45   ./configure # okay there are setting the paths for me - saves me a job
  11  21:46   make # like fairytale stuff for a load of C scripts
  16  21:49   ls | grep samtools # I wanna know if its compiled and I see samtools* ... yep
  17  21:49   ln -s ./samtools* ~/bin # I'm gonna pop a link in my bin so after I type
  18  21:49   rehash # 'cause I still insist on tcsh rather than bash (don't do it in bash)
  </code></pre>
  
  <p>However, the following is a bit creepy because I get loads of perl scripts in my /usr/local/bin ...</p>
  
  <pre><code>make install
  </code></pre>
  
  <p>Anyway,</p>
  
  <pre><code>samtools
  </code></pre>
  
  <p>It took 4 mins on an OS X machine, using tsch, after I just quaffed 2 pints at my  pub (10pm London time). So probability is set against me .... </p>
  
  <p><strong>OUTPUT</strong></p>
  
  <pre><code>Program: samtools (Tools for alignments in the SAM format)
  Version: 0.1.18 (r982:295)
  
  Usage:   samtools &lt;command&gt; [options]
  
  Command: view        SAM&lt;-&gt;BAM conversion
           sort        sort alignment file
           mpileup     multi-way pileup
           depth       compute the depth
           faidx       index/extract FASTA
           tview       text alignment viewer
           index       index alignment
           idxstats    BAM index stats (r595 or later)
  </code></pre>
  
  <p>etc ...
  BTW seriously, fun over, avoid "<code>sudo</code>" if you can, for lots of reasons (which I'm not gonna explain). Its a last resort and usually means your paths are incorrectly set.</p>
  
  <p>sudo will be refused on a remote machine, without question. You COULD ask systems admin to do this for you. HOWEVER, I'd try and install yourself without <code>sudo</code> and your bioinformatics will benefit.</p>
  
  <hr>
  
  <pre><code>Program: samtools (Tools for alignments in the SAM format)
  Version: 1.9 (using htslib 1.9)
  
  Usage:   samtools &lt;command&gt; [options]
  
  Commands:
    -- Indexing
       dict           create a sequence dictionary file
       faidx          index/extract FASTA
       fqidx          index/extract FASTQ
       index          index alignment
  </code></pre>
  
  <p><strong>Output</strong> following <code>make install</code></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-02-13T08:08:02.723Z
Answers.Text: 0.1.18 is a truly ancient version of samtools and is unlikely to be what you compiled.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-02-13T15:34:28.797Z
Answers.Text: Yes you are right, currently 1.9 (above)
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-02-12T22:05:09.693Z
Answers.LastActivityDate: 2019-02-13T15:33:53.453Z
Answers.LastEditDate: 2019-02-13T15:33:53.453Z
Answers.UserDisplayName: M__
Body: <p>I am new to bash and the processes behind cluster computing in general and need some help with understanding some basics.</p>
  
  <p>After looking all over the internet and this forum (+ askUbuntu) I found nothing that addresses this issue.</p>
  
  <p>I have a series of raw RNA sequencing files: .bam and wish to utilize samtools (or others) to begin the data preprocessing steps defined in many workflows.</p>
  
  <p>I have installed samtools and many other programs necessary for the workflow, however, once I am on the remote server in bash, and try and run a function over the files of interest, it gives me the error: <code>-bash-samtools: command not found</code></p>
  
  <p>When I try to install the package, say samtools, by running <code>sudo apt install samtools</code>, I get an error stating I do not have permission to do such.</p>
  
  <p>What do I do? Must I bring up this issue to the server provider or is there a way around it?</p>
  
  <p>Thank you for your time,</p>
  
Tags: <rna-seq><scrnaseq><samtools><bash>
Title: Using preprocessing/alignment functions on the server
ThreadText: # Using preprocessing/alignment functions on the server
  
  (Asked by: username_0 on 2019-02-12)
  
  I am new to bash and the processes behind cluster computing in general and need some help with understanding some basics.
  
  After looking all over the internet and this forum (+ askUbuntu) I found nothing that addresses this issue.
  
  I have a series of raw RNA sequencing files: .bam and wish to utilize samtools (or others) to begin the data preprocessing steps defined in many workflows.
  
  I have installed samtools and many other programs necessary for the workflow, however, once I am on the remote server in bash, and try and run a function over the files of interest, it gives me the error: `-bash-samtools: command not found`
  
  When I try to install the package, say samtools, by running `sudo apt install samtools`, I get an error stating I do not have permission to do such.
  
  What do I do? Must I bring up this issue to the server provider or is there a way around it?
  
  Thank you for your time,
  
  **Tags:** rna-seq, scrnaseq, samtools, bash
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2019-02-12. Score: 3 | Accepted answer
  
  The short answer is to [use conda](https://docs.conda.io/en/latest/miniconda.html). In the [bioconda channel](https://bioconda.github.io/) we have most of the tools used in bioinformatics, such as samtools. You do not need administrator permissions to install conda or packages with it, so your lack of `sudo` ability is not an issue.
  
  > I have installed samtools and many other programs necessary for the workflow, however, once I am on the remote server in bash, and try and run a function over the files of interest, it gives me the error
  
  Installing packages on your local machine won't affect the remote server unless they share a file system, so this is expected.
  
  As an aside, BAM files aren't really "raw", they're considered processed data (fastq/fast5 files are considered truly "raw" data in the sequencing world).
  
  
  ---
  
  ### Answer by username_2 on 2019-02-12. Score: 2
  
  At a very wild guess
  
  ```
  -bash-samtools
  
  ```
  
  This looks shaky. For a start you need a space between the command and the application in all Linux/Unix/Mac OS X applications (its complicated to explain right now [see below] just accept it).
  
  ---
  
  Wait you are using `sudo` and thats how you are installing on a local machine. `sudo` on a remote machine will never work, because you are not the systems admin. `sudo` on a local machine is not cool (see below)
  
  ---
  
  Anyway I need to do some next-gen and have 6 MiSeq kits waiting for action so I installed it from here:
  <http://www.htslib.org/download/>
  
  Okay so here's my tcsh history
  
  ```
   4  21:44   cd sam* # like I was in the Desktop
   7  21:44   more README # I needed to know how they wanted the installation
   8  21:45   ./configure # okay there are setting the paths for me - saves me a job
  11  21:46   make # like fairytale stuff for a load of C scripts
  16  21:49   ls | grep samtools # I wanna know if its compiled and I see samtools* ... yep
  17  21:49   ln -s ./samtools* ~/bin # I'm gonna pop a link in my bin so after I type
  18  21:49   rehash # 'cause I still insist on tcsh rather than bash (don't do it in bash)
  
  ```
  
  However, the following is a bit creepy because I get loads of perl scripts in my /usr/local/bin ...
  
  ```
  make install
  
  ```
  
  Anyway,
  
  ```
  samtools
  
  ```
  
  It took 4 mins on an OS X machine, using tsch, after I just quaffed 2 pints at my pub (10pm London time). So probability is set against me ....
  
  **OUTPUT**
  
  ```
  Program: samtools (Tools for alignments in the SAM format)
  Version: 0.1.18 (r982:295)
  
  Usage:   samtools <command> [options]
  
  Command: view        SAM<->BAM conversion
           sort        sort alignment file
           mpileup     multi-way pileup
           depth       compute the depth
           faidx       index/extract FASTA
           tview       text alignment viewer
           index       index alignment
           idxstats    BAM index stats (r595 or later)
  
  ```
  
  etc ...
  BTW seriously, fun over, avoid "`sudo`" if you can, for lots of reasons (which I'm not gonna explain). Its a last resort and usually means your paths are incorrectly set.
  
  sudo will be refused on a remote machine, without question. You COULD ask systems admin to do this for you. HOWEVER, I'd try and install yourself without `sudo` and your bioinformatics will benefit.
  
  ---
  
  ```
  Program: samtools (Tools for alignments in the SAM format)
  Version: 1.9 (using htslib 1.9)
  
  Usage:   samtools <command> [options]
  
  Commands:
    -- Indexing
       dict           create a sequence dictionary file
       faidx          index/extract FASTA
       fqidx          index/extract FASTQ
       index          index alignment
  
  ```
  
  **Output** following `make install`
  
  > **Comments:**
  > **username_1**: 0.1.18 is a truly ancient version of samtools and is unlikely to be what you compiled.  
  > **username_2**: Yes you are right, currently 1.9 (above)  
  
  ---
  
  