Question

我有一个shell脚本：

   /**
 * this will convert the whole json into map which you can use to determine the json elements
 *
 * @param json
 */
private void getModelFromJson(JsonObject json) {
    Gson gson = new Gson();
    Map<String, JsonElement> jsonElementMap = gson.fromJson(json.toString(), new TypeToken<Map<String, JsonElement>>() {
    }.getType());
    for (Map.Entry<String, JsonElement> jsonElementEntry : jsonElementMap.entrySet()) {
        if (jsonElementEntry.getValue().isJsonPrimitive()) {
            //json primitives are data types, do something
            //get json boolean
            //you can here also check if json element has some json object or json array or primitives based on that
            //you can convert this to something else after comparison
            if (true) {
                InterestModelResponse response = gson.fromJson(jsonElementEntry.getValue().getAsJsonObject().toString(), InterestModelResponse.class);
                //use your dynamic converted model
            }
        } else {
            //do something else
        }
    }

}

当我在hpc（qsub）上运行脚本时，它会返回错误日志：

#!/bin/bash

source activate nanopore_py3

REF=/mnt/projects/lich/stooldrug/iRep_temp/co_growth/MG1655.fasta

iRep -f $REF -s MMF064_HS006/MMF064_2.sam -o MMF064.iRep

奇怪的是，当我在终端上运行/opt/p6444/n121/job_scripts/19745189: line 3: activate: No such file or directory /opt/p6444/n121/job_scripts/19745189: line 7: iRep: command not found时，一切正常。我还在$ PATH中添加了source命令的路径。

有人可以帮忙吗？

Answer 1

您的脚本在其自己的外壳环境中运行，因此不了解您环境中的PATH变量。您需要在脚本中设置PATH，并包括要执行的程序的位置。

#!/bin/bash

export PATH=$PATH:/some/path/bin

source activate nanopore_py3

# ...

或者，您可以source完整路径：

source /some/path/activate /other/path/nanopore_py3

命令在bash中有效，但在脚本中无效

1 个答案: