Answers.Body: <p>As noted by the comments and the SLURM manual (not so much bioinformatics related?)</p>
  
  <p>You need the following terms in your batch/queuing command:</p>
  
  <pre><code>--mail-type=ALL
  --mail-user=you@email.com
  </code></pre>
  
  <p>I used "ALL" which will send you <em>all</em> reports. If you just want the finish message then you would use "END" and "FAIL" like such:</p>
  
  <pre><code>--mail-type=END,FAIL
  </code></pre>
  
  <p>Here are the specifics from the <a href="https://slurm.schedmd.com/sbatch.html" rel="nofollow noreferrer">manual</a> if you wish to make a different selection:</p>
  
  <p><strong>--mail-type=</strong></p>
  
  <blockquote>
    <p>Notify user by email when certain event types occur. Valid type values
    are NONE, BEGIN, END, FAIL, REQUEUE, ALL (equivalent to BEGIN, END,
    FAIL, REQUEUE, and STAGE_OUT), STAGE_OUT (burst buffer stage out and
    teardown completed), TIME_LIMIT, TIME_LIMIT_90 (reached 90 percent of
    time limit), TIME_LIMIT_80 (reached 80 percent of time limit),
    TIME_LIMIT_50 (reached 50 percent of time limit) and ARRAY_TASKS (send
    emails for each array task). Multiple type values may be specified in
    a comma separated list. The user to be notified is indicated with
    --mail-user. Unless the ARRAY_TASKS option is specified, mail notifications on job BEGIN, END and FAIL apply to a job array as a
    whole rather than generating individual email messages for each task
    in the job array.</p>
  </blockquote>
  
  <p><strong>--mail-user=</strong></p>
  
  <blockquote>
    <p>User to receive email notification of state changes as defined by
    --mail-type. The default value is the submitting user.</p>
  </blockquote>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-03-15T14:09:51.257Z
Answers.LastActivityDate: 2019-03-15T14:09:51.257Z
Answers.UserDisplayName: story
Body: <p>I am working on a SLURM-based cluster. I am currently using the following slurm json file:</p>
  
  <pre><code>{
      "__default__" :
      {
          "A" : "overall",
          "time" : "96:00:00",
          "nodes": 1,
          "ntasks": 1,
          "cpus" : 24,
          "p" : "LONG",
          "mem": 16G,
          "output": "snakemake%A.out",
          "error": "snakemake%A.err"
      }
  }
  </code></pre>
  
  <p>along with the following command:</p>
  
  <pre><code>snakemake --jobs 200 --use-conda --printshellcmds  --cluster-config slurm.json --cluster "sbatch -A {cluster.A} -p {cluster.p} -t {cluster.time} --output {cluster.output} --error {cluster.error} --ntasks {cluster.ntasks} --cpus-per-task {cluster.cpus} --mem {cluster.mem}"
  </code></pre>
  
  <p>I would like to be able to specify my email and receive an email when a job finishes. I have tried adding a line in the json file with <code>"email": my@email.com</code> and an option to the sbatch command <code>--email {cluster.email}</code> but that did not work.</p>
  
  <p>Anyone knows how to do it?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-03-11T23:13:33.057Z
Comments.Text: After looking at some headers of files (`#SBATCH --mail-user=email@com`I have used `--mail-user` instead. I'll let you know if I receive an email.
Comments.UserDisplayName: Biomagician
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-03-12T07:55:37.367Z
Comments.Text: I'd be surprised if [--mail-user](https://github.com/dpryan79/Misc/blob/master/MPIIE_internal/SlurmEasy#L85-L90) didn't end up working. Note also `--mail-type`.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-03-16T15:48:15.603Z
Comments.Text: so --mail-user on its own didn't work but by adding the --mail-type, it worked!
Comments.UserDisplayName: Biomagician
Tags: <snakemake><slurm>
Title: How can I specify an email address in the SLURM snakemake json configuration file?
ThreadText: # How can I specify an email address in the SLURM snakemake json configuration file?
  
  (Asked by: username_0 on 2019-03-11)
  
  I am working on a SLURM-based cluster. I am currently using the following slurm json file:
  
  ```
  {
      "__default__" :
      {
          "A" : "overall",
          "time" : "96:00:00",
          "nodes": 1,
          "ntasks": 1,
          "cpus" : 24,
          "p" : "LONG",
          "mem": 16G,
          "output": "snakemake%A.out",
          "error": "snakemake%A.err"
      }
  }
  
  ```
  
  along with the following command:
  
  ```
  snakemake --jobs 200 --use-conda --printshellcmds  --cluster-config slurm.json --cluster "sbatch -A {cluster.A} -p {cluster.p} -t {cluster.time} --output {cluster.output} --error {cluster.error} --ntasks {cluster.ntasks} --cpus-per-task {cluster.cpus} --mem {cluster.mem}"
  
  ```
  
  I would like to be able to specify my email and receive an email when a job finishes. I have tried adding a line in the json file with `"email": my@email.com` and an option to the sbatch command `--email {cluster.email}` but that did not work.
  
  Anyone knows how to do it?
  
  **Tags:** snakemake, slurm
  
  > **Comments:**
  > **username_0**: After looking at some headers of files (`#SBATCH --mail-user=email@com`I have used `--mail-user` instead. I'll let you know if I receive an email.  
  > **username_1**: I'd be surprised if [--mail-user](https://github.com/dpryan79/Misc/blob/master/MPIIE_internal/SlurmEasy#L85-L90) didn't end up working. Note also `--mail-type`.  
  > **username_0**: so --mail-user on its own didn't work but by adding the --mail-type, it worked!  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2019-03-15. Score: 4 | Accepted answer
  
  As noted by the comments and the SLURM manual (not so much bioinformatics related?)
  
  You need the following terms in your batch/queuing command:
  
  ```
  --mail-type=ALL
  --mail-user=you@email.com
  
  ```
  
  I used "ALL" which will send you *all* reports. If you just want the finish message then you would use "END" and "FAIL" like such:
  
  ```
  --mail-type=END,FAIL
  
  ```
  
  Here are the specifics from the [manual](https://slurm.schedmd.com/sbatch.html) if you wish to make a different selection:
  
  **--mail-type=**
  
  > Notify user by email when certain event types occur. Valid type values
  > are NONE, BEGIN, END, FAIL, REQUEUE, ALL (equivalent to BEGIN, END,
  > FAIL, REQUEUE, and STAGE\_OUT), STAGE\_OUT (burst buffer stage out and
  > teardown completed), TIME\_LIMIT, TIME\_LIMIT\_90 (reached 90 percent of
  > time limit), TIME\_LIMIT\_80 (reached 80 percent of time limit),
  > TIME\_LIMIT\_50 (reached 50 percent of time limit) and ARRAY\_TASKS (send
  > emails for each array task). Multiple type values may be specified in
  > a comma separated list. The user to be notified is indicated with
  > --mail-user. Unless the ARRAY\_TASKS option is specified, mail notifications on job BEGIN, END and FAIL apply to a job array as a
  > whole rather than generating individual email messages for each task
  > in the job array.
  
  **--mail-user=**
  
  > User to receive email notification of state changes as defined by
  > --mail-type. The default value is the submitting user.
  
  
  ---
  
  