Answers.Body: <p>Given the Makefile you provided and which someone then deleted from the question, you should probably just add this line (this should be the first rule):</p>
  
  <p><code>rule all: input: ["data/{}/genome.fa.gz".format(x) for x in species.split()]
  </code></p>
  
  <p>This rule just specifies a list of expected output files and corresponds to the following lines from the original <code>Makefile</code>:</p>
  
  <p><code>GENOMES=$(patsubst %, data/%/genome.fa.gz, $(SPECIES))
  all : $(GENOMES)</code></p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-05T11:50:03.777Z
Answers.Text: I have deleted Make equivalent since was not really related to the problem.
Answers.UserDisplayName: Kamil S Jaron
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Answers.CreationDate: 2017-11-03T18:01:05.533Z
Answers.LastActivityDate: 2017-11-03T18:01:05.533Z
Answers.UserDisplayName: Karel Břinda
Answers.Body: <p>The problem is that you need a master rule that requires all of your desired outputs as inputs, in your case it would be :</p>
  
  <pre><code>rule all:
      input:
          expand("data/{sp}/genome.fa.gz", sp=species.split(' '))
  </code></pre>
  
  <p>You'll also need separate download link inputs for each species. You could make a separate <code>download_table.tsv</code> for each species, but it would probably be easier to make a config file with this information, and add a params keyword to your rule. Something like:</p>
  
  <pre><code>rule download:
     params:
         url=config['locations']['sp']
     output :
         "data/{sp}/genome.fa.gz"
     shell :
         "scripts/download.sh {params.url}"
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-03T15:45:53.367Z
Answers.Text: I wouldn't erase it if I were you. A lot of people get confused about Snakemake error messages, so its helpful to have some examples on here.
Answers.UserDisplayName: heathobrien
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-03T15:47:27.163Z
Answers.Text: Then I will at least dramatically edit it. (I try to do it in a way so your answer still fits)
Answers.UserDisplayName: Kamil S Jaron
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Answers.CreationDate: 2017-11-03T19:13:25.243Z
Answers.Text: @KamilSJaron I agree the question should be kept, but maybe change the title to reflect the error message, this has nothing to do with NCBI
Answers.UserDisplayName: Chris_Rands
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-06T10:51:58.353Z
Answers.Text: Also note that Snakemake has an NCBI remote provider: http://snakemake.readthedocs.io/en/stable/snakefiles/remote_files.html#genbank-ncbi-entrez
Answers.UserDisplayName: Johannes Köster
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-10T15:53:09.563Z
Answers.Text: @JohannesKöster I was looking at it. But since I could not make it work without remote I have not even tried with remote. And then the problem I originally had with non-remote solution is very much unrelated to downloading of sequences. It's a good tip though, maybe work an answer?
Answers.UserDisplayName: Kamil S Jaron
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Answers.CreationDate: 2017-11-03T12:49:58.650Z
Answers.LastActivityDate: 2017-11-05T11:52:23.763Z
Answers.LastEditDate: 2017-11-05T11:52:23.763Z
Answers.UserDisplayName: heathobrien
Body: <p>I would like to do easily reproducible analysis using publicly available data from NCBI, so I have chosen a <code>snakemake</code>. </p>
  
  <p>I would like to write a single rule, that would be able to download any genome given a species code name and separated table of species and their NCBI IDs. So I wrote a script <code>scripts/download.sh</code> that takes a species code and download the genome to <code>data/&lt;species_code&gt;/genome.fa.gz</code>. The script internally reads the table <code>tables/download_table.tsv</code>, where are corresponding species code names and NCBI IDs.</p>
  
  <p>So I tried to do a <code>snakemake</code> like this :</p>
  
  <pre><code>species='Cbir Avag Fcan Lcla Dcor Dpac Pdav Psp62 Psp79 Minc1 Minc2 Mjav Mare Mflo Mhap Pant'
  
  rule download:
      input :
          "tables/download_table.tsv"
      output :
          "data/{sp}/genome.fa.gz"
      shell :
          "scripts/download.sh {sp}"
  </code></pre>
  
  <p>However, <code>snakemake</code> returned an error message I do not really understand :</p>
  
  <pre><code>Target rules may not contain wildcards. Please specify concrete files or a rule without wildcards.`. 
  </code></pre>
  
  <p>Is there a way to write a single rule for downloading all the genomes?</p>
  
Tags: <snakemake>
Title: How to resolve in snakemake error : "Target rules may not contain wildcards."
ThreadText: # How to resolve in snakemake error : "Target rules may not contain wildcards."
  
  (Asked by: username_0 on 2017-11-03)
  
  I would like to do easily reproducible analysis using publicly available data from NCBI, so I have chosen a `snakemake`.
  
  I would like to write a single rule, that would be able to download any genome given a species code name and separated table of species and their NCBI IDs. So I wrote a script `scripts/download.sh` that takes a species code and download the genome to `data/<species_code>/genome.fa.gz`. The script internally reads the table `tables/download_table.tsv`, where are corresponding species code names and NCBI IDs.
  
  So I tried to do a `snakemake` like this :
  
  ```
  species='Cbir Avag Fcan Lcla Dcor Dpac Pdav Psp62 Psp79 Minc1 Minc2 Mjav Mare Mflo Mhap Pant'
  
  rule download:
      input :
          "tables/download_table.tsv"
      output :
          "data/{sp}/genome.fa.gz"
      shell :
          "scripts/download.sh {sp}"
  
  ```
  
  However, `snakemake` returned an error message I do not really understand :
  
  ```
  Target rules may not contain wildcards. Please specify concrete files or a rule without wildcards.`. 
  
  ```
  
  Is there a way to write a single rule for downloading all the genomes?
  
  **Tags:** snakemake
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2017-11-03. Score: 9 | Accepted answer
  
  The problem is that you need a master rule that requires all of your desired outputs as inputs, in your case it would be :
  
  ```
  rule all:
      input:
          expand("data/{sp}/genome.fa.gz", sp=species.split(' '))
  
  ```
  
  You'll also need separate download link inputs for each species. You could make a separate `download_table.tsv` for each species, but it would probably be easier to make a config file with this information, and add a params keyword to your rule. Something like:
  
  ```
  rule download:
     params:
         url=config['locations']['sp']
     output :
         "data/{sp}/genome.fa.gz"
     shell :
         "scripts/download.sh {params.url}"
  
  ```
  
  > **Comments:**
  > **username_2**: I wouldn't erase it if I were you. A lot of people get confused about Snakemake error messages, so its helpful to have some examples on here.  
  > **username_0**: Then I will at least dramatically edit it. (I try to do it in a way so your answer still fits)  
  > **username_3**: @username_0 I agree the question should be kept, but maybe change the title to reflect the error message, this has nothing to do with NCBI  
  > **username_4**: Also note that Snakemake has an NCBI remote provider: http://snakemake.readthedocs.io/en/stable/snakefiles/remote_files.html#genbank-ncbi-entrez  
  > **username_0**: @username_4 I was looking at it. But since I could not make it work without remote I have not even tried with remote. And then the problem I originally had with non-remote solution is very much unrelated to downloading of sequences. It's a good tip though, maybe work an answer?  
  
  ---
  
  ### Answer by username_1 on 2017-11-03. Score: 3
  
  Given the Makefile you provided and which someone then deleted from the question, you should probably just add this line (this should be the first rule):
  
  `rule all: input: ["data/{}/genome.fa.gz".format(x) for x in species.split()]`
  
  This rule just specifies a list of expected output files and corresponds to the following lines from the original `Makefile`:
  
  `GENOMES=$(patsubst %, data/%/genome.fa.gz, $(SPECIES))
  all : $(GENOMES)`
  
  > **Comments:**
  > **username_0**: I have deleted Make equivalent since was not really related to the problem.  
  
  ---
  
  